spades_biosyntheticspades: macros.xml annotate

annotate macros.xml @ 0:42a39792aaae draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"

author	iuc
date	Sun, 23 Jan 2022 21:35:21 +0000
parents
children	8a9a9350ffaf

rev	line source
0 42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	1 <macros>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	2 <token name="@TOOL_VERSION@">3.15.3</token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	3 <token name="@VERSION_SUFFIX@">0</token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	4 <xml name="requirements">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	5 <requirements>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	6 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	7 <requirement type="package" version="3.0">zip</requirement>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	8 <yield/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	9 </requirements>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	10 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	11 <xml name="stdio">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	12 <stdio>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	13 <exit_code range="1:"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	14 <regex match="Cannot allocate memory"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	15 source="stdout"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	16 level="fatal_oom"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	17 description="Out of memory error occurred"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	18 <regex match="The reads contain too many k-mers to fit into available memory"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	19 source="stdout"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	20 level="fatal_oom"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	21 description="Out of memory error occurred"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	22 </stdio>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	23 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	24 <xml name="version_command">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	25 <version_command><![CDATA[spades.py --version 2>&1 \| awk -F 'v' '{print $2}']]></version_command>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	26 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	27 <token name="@INTYPES@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	28
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	29 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	30 <xml name="citations">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	31 <citations>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	32 <citation type="doi">10.1093/bioinformatics/btv688</citation>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	33 <citation type="doi">10.1093/bioinformatics/btu266</citation>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	34 <citation type="doi">10.1093/bioinformatics/btv337</citation>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	35 <yield/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	36 </citations>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	37 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	38 <xml name="operation_mode" token_help="">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	39 <param name="operation_mode" type="select" label="Operation mode" help="@HELP@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	40 <option value="">Assembly and error correction</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	41 <option value="--only-assembler">Only assembler (--only-assembler)</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	42 <option value="--only-error-correction">Only error correction (--only-error-correction)</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	43 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	44 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	45
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	46
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	47 <!-- PREPARE INPUT FILES-->
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	48
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	49 <token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	50 #if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	51 mkdir -p reads1 &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	52 #set file_paths1 = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	53 #for $input_file in $singlePaired.input1
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	54 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	55 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	56 #set $file_path = 'reads1/' + $fname
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	57 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	58 $file_paths1.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	59 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	60 #else if $singlePaired.sPaired == "paired"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	61 mkdir -p paired_reads1 &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	62 #set fw_reads1 = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	63 #for $input_file in $singlePaired.input1
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	64 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	65 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	66 #set $file_path = 'paired_reads1/' + str($fname)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	67 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	68 $fw_reads1.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	69 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	70 #set rv_reads1 = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	71 #for $input_file in $singlePaired.input2
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	72 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	73 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	74 #set $file_path = 'paired_reads1/' + str($fname)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	75 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	76 $rv_reads1.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	77 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	78 #silent $fw_reads1.sort()
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	79 #silent $rv_reads1.sort()
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	80 #else
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	81 mkdir -p paired_reads1 &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	82 #set fw_reads1 = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	83 #set rv_reads1 = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	84 #for $i, $input_file in enumerate($singlePaired.input)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	85 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	86 #set $file_path = 'paired_reads1/fw' + str($i) + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	87 ln -s '$input_file.forward' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	88 $fw_reads1.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	89 #set $file_path = 'paired_reads1/rv' + str($i) + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	90 ln -s '$input_file.reverse' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	91 $rv_reads1.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	92 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	93 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	94 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	95
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	96 <token name="@PREPROCESS_INPUT_FILES_ADDITIONAL@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	97 #if $additional_reads.singlePaired.sPaired == "single" or $additional_reads.singlePaired.sPaired == "paired_interlaced"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	98 mkdir -p reads2 &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	99 #set file_paths2 = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	100 #for $input_file in $additional_reads.singlePaired.input1
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	101 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	102 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	103 #set $file_path = 'reads2/' + $fname
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	104 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	105 $file_paths2.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	106 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	107 #else if $additional_reads.singlePaired.sPaired == "paired"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	108 mkdir -p paired_reads2 &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	109 #set fw_reads2 = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	110 #for $input_file in $additional_reads.singlePaired.input1
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	111 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	112 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	113 #set $file_path = 'paired_reads2/' + str($fname)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	114 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	115 $fw_reads2.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	116 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	117 #set rv_reads2 = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	118 #for $input_file in $additional_reads.singlePaired.input2
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	119 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	120 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	121 #set $file_path = 'paired_reads2/' + str($fname)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	122 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	123 $rv_reads2.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	124 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	125 #silent $fw_reads2.sort()
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	126 #silent $rv_reads2.sort()
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	127 #else
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	128 mkdir -p paired_reads2 &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	129 #set fw_reads2 = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	130 #set rv_reads2 = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	131 #for $i, $input_file in enumerate($additional_reads.singlePaired.input)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	132 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	133 #set $file_path = 'paired_reads2/fw' + str($i) + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	134 ln -s '$input_file.forward' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	135 $fw_reads2.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	136 #set $file_path = 'paired_reads2/rv' + str($i) + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	137 ln -s '$input_file.reverse' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	138 $rv_reads2.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	139 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	140 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	141 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	142
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	143 <!-- COMMANDS -->
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	144
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	145 <token name="@RESOURCES@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	146 -t \${GALAXY_SLOTS:-4}
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	147 -m \${GALAXY_MEMORY_GB:-8}
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	148 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	149
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	150 <token name="@INPUT_READS_MAIN@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	151 #if $singlePaired.sPaired == "single"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	152 #for $read in $file_paths1
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	153 --s $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	154 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	155 #else if $singlePaired.sPaired == "paired"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	156 #for $read in $fw_reads1
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	157 --${singlePaired.type_paired}-1 $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	158 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	159 #for $read in $rv_reads1
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	160 --${singlePaired.type_paired}-2 $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	161 --${singlePaired.type_paired}-or $library $singlePaired.orientation
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	162 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	163 #else if $singlePaired.sPaired == "paired_interlaced"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	164 #for $read in $file_paths1
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	165 --${singlePaired.type_paired}-12 $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	166 --${singlePaired.type_paired}-or $library $singlePaired.orientation
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	167 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	168 #else
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	169 #for $read in $fw_reads1
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	170 --${singlePaired.type_paired}-1 $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	171 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	172 #for $read in $rv_reads1
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	173 --${singlePaired.type_paired}-2 $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	174 --${singlePaired.type_paired}-or $library $singlePaired.orientation
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	175 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	176 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	177 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	178
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	179
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	180 <token name="@INPUT_READS_ADDITIONAL@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	181 @LIBRARY_NUMBER@
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	182 #if $additional_reads.singlePaired.sPaired == "single"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	183 #for $read in $file_paths2
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	184 --s $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	185 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	186 #else if $additional_reads.singlePaired.sPaired == "paired"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	187 #for $read in $fw_reads2
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	188 --${additional_reads.singlePaired.type_paired}-1 $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	189 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	190 #for $read in $rv_reads2
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	191 --${additional_reads.singlePaired.type_paired}-2 $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	192 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	193 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	194 #else if $additional_reads.singlePaired.sPaired == "paired_interlaced"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	195 #for $read in $file_paths2
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	196 --${additional_reads.singlePaired.type_paired}-12 $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	197 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	198 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	199 #else
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	200 #for $read in $fw_reads2
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	201 --${additional_reads.singlePaired.type_paired}-1 $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	202 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	203 #for $read in $rv_reads2
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	204 --${additional_reads.singlePaired.type_paired}-2 $library '${read}'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	205 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	206 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	207 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	208 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	209
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	210 <token name="@PIPELINE_OPTIONS@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	211 #for $i in $mode_sel
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	212 $i
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	213 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	214 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	215
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	216 <token name="@KMER@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	217 #if $kmer_cond.kmer_sel != 'auto'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	218 -k '$kmer_cond.manual'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	219 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	220 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	221
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	222 <token name="@PHREDOFFSET@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	223 #if $phred_offset != 'auto'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	224 --phred-offset $phred_offset
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	225 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	226 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	227
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	228 <!-- ADDITIONAL INPUTS-->
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	229
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	230 <token name="@PREPROCESS_CONTIGS_FILES@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	231 #if $arf.trusted_contigs
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	232 mkdir -p trusted_contigs &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	233 #set trusted_contigs = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	234 #for $i, $input_file in enumerate($arf.trusted_contigs,1)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	235 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	236 #set $fname = 'file' + str($i) + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	237 #set $file_path = 'trusted_contigs/' + $fname
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	238 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	239 $trusted_contigs.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	240 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	241 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	242 #if $arf.untrusted_contigs
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	243 mkdir -p untrusted_contigs &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	244 #set untrusted_contigs = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	245 #for $i, $input_file in enumerate($arf.untrusted_contigs,1)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	246 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	247 #set $fname = 'file' + str($i) + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	248 #set $file_path = 'untrusted_contigs/' + $fname
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	249 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	250 $untrusted_contigs.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	251 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	252 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	253 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	254
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	255 <token name="@PREPROCESS_NANOPORE_PACBIO_FILES@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	256 #if $arf.nanopore
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	257 mkdir -p nanopore_reads &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	258 #set nanopore_reads = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	259 #for $i, $input_file in enumerate($arf.nanopore,1)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	260 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	261 #set $fname = 'file' + str($i) + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	262 #set $file_path = 'nanopore_reads/' + $fname
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	263 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	264 $nanopore_reads.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	265 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	266 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	267 #if $arf.pacbio
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	268 mkdir -p pacbio_reads &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	269 #set pacbio_reads = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	270 #for $i, $input_file in enumerate($arf.pacbio,1)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	271 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	272 #set $fname = 'file' + str($i) + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	273 #set $file_path = 'pacbio_reads/' + $fname
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	274 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	275 $pacbio_reads.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	276 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	277 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	278 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	279
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	280 <token name="@PREPROCESS_SANGER_FILES@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	281 #if $arf.sanger
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	282 mkdir -p sanger_reads &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	283 #set sanger_reads = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	284 #for $i, $input_file in enumerate($arf.sanger,1)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	285 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	286 #set $fname = 'file' + str($i) + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	287 #set $file_path = 'sanger_reads/' + $fname
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	288 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	289 $sanger_reads.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	290 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	291 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	292 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	293
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	294 <token name="@PREPROCESS_FL_RNA_FILES@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	295 #if $arf.flrna
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	296 mkdir -p flrna_reads &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	297 #set flrna_reads = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	298 #for $i, $input_file in enumerate($arf.flrna,1)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	299 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	300 #set $fname = 'file' + str($i) + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	301 #set $file_path = 'flrna_reads/' + $fname
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	302 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	303 $flrna_reads.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	304 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	305 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	306 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	307
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	308 <token name="@PREPROCESS_ASSEMBLY_GRAPH_FILES@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	309 #if $arf.assembly_graph
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	310 mkdir -p assembly_graphs &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	311 #set assembly_graphs = []
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	312 #for $i, $input_file in enumerate($arf.assembly_graph,1)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	313 #set $ext = $input_file.ext.replace('gfa1', 'gfa')
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	314 #set $fname = 'file' + str($i) + '.' + $ext
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	315 #set $file_path = 'assembly_graphs/' + $fname
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	316 ln -s '$input_file' $file_path &&
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	317 $assembly_graphs.append($file_path)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	318 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	319 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	320 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	321
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	322
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	323 <token name="@NANOPORE_PACBIO@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	324 #if $arf.nanopore
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	325 #for $read in $nanopore_reads
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	326 --nanopore $read
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	327 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	328 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	329 #if $arf.pacbio
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	330 #for $read in $pacbio_reads
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	331 --pacbio $read
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	332 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	333 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	334 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	335
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	336
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	337 <token name="@SANGER@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	338 #if $arf.sanger
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	339 #for $read in $sanger_reads
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	340 --sanger $read
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	341 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	342 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	343 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	344
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	345 <token name="@FL_RNA@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	346 #if $arf.flrna
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	347 #for $read in $flrna_reads
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	348 --fl-rna $read
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	349 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	350 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	351 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	352
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	353 <token name="@ASSEMBLY_GRAPH@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	354 #if $arf.assembly_graph
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	355 #for $graph in $assembly_graphs
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	356 --assembly-graph $graph
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	357 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	358 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	359 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	360
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	361 <token name="@CONTIGS@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	362 #if $arf.trusted_contigs
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	363 #for $read in $trusted_contigs
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	364 --trusted-contigs $read
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	365 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	366 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	367 #if $arf.untrusted_contigs
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	368 #for $read in $untrusted_contigs
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	369 --untrusted-contigs $read
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	370 #end for
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	371 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	372 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	373
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	374 <token name="@LIBRARY_NUMBER@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	375 #if $additional_reads.selector == 'true' and $additional_reads.library_number == 'false'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	376 #set $library += 1
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	377 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	378 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	379
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	380 <!-- POSTPROCESSING -->
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	381
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	382 <token name="@STATS@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	383 #if 'cs' in $optional_output
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	384 && test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' \|\| echo 'No contigs.fasta.'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	385 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	386 #if 'ss' in $optional_output
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	387 && test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' \|\| echo 'No scaffolds.fasta.'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	388 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	389 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	390
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	391 <token name="@CORRECTED@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	392 #if 'corrected' in $optional_output
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	393 && test -d 'output/corrected' && zip -q -r 'corrected.zip' 'output/corrected/*.fastq.gz' \|\| echo 'No output files for corrected reads.'
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	394 #end if
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	395 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	396
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	397 <!--
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	398 input
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	399 -->
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	400
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	401 <xml name="input_files_all" token_format="" token_label="" token_help="It assumes that all samples belong to the same library. If you want to use samples from two different libraries, include the second library as additional set of short-reads.">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	402 <conditional name="singlePaired">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	403 <param name="sPaired" type="select" label="Single-end or paired-end short-reads" help="@HELP@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	404 <option value="single" selected="true">Single-end</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	405 <option value="paired">Paired-end: individual datasets</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	406 <option value="paired_interlaced">Paired-end: interlaced reads</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	407 <option value="paired_collection">Paired-end: list of dataset pairs</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	408 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	409 <when value="single">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	410 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	411 </when>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	412 <when value="paired">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	413 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: forward reads"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	414 <param format="@FORMAT@" name="input2" type="data" multiple="true" label="@LABEL@: reverse reads"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	415 <expand macro="type_paired"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	416 <expand macro="orientation"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	417 </when>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	418 <when value="paired_interlaced">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	419 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	420 <expand macro="type_paired"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	421 <expand macro="orientation"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	422 </when>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	423 <when value="paired_collection">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	424 <param format="@FORMAT@" name="input" type="data_collection" collection_type="list:paired" label="@LABEL@: collection"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	425 <expand macro="type_paired"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	426 <expand macro="orientation"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	427 </when>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	428 </conditional>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	429 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	430
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	431 <xml name="input_files_paired" token_format="" token_label="" token_help="It assumes that all samples belong to the same library. If you want to use samples from two different libraries, include the second library as additional set of short-reads.">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	432 <conditional name="singlePaired">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	433 <param name="sPaired" type="select" label="Pair-end reads input format" help="@HELP@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	434 <option value="paired" selected="true">Paired-end: individual datasets</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	435 <option value="paired_interlaced">Paired-end: interlaced reads</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	436 <option value="paired_collection">Paired-end: list of dataset pairs</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	437 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	438 <when value="paired">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	439 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: forward reads"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	440 <param format="@FORMAT@" name="input2" type="data" multiple="true" label="@LABEL@: reverse reads"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	441 <expand macro="type_paired"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	442 <expand macro="orientation"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	443 </when>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	444 <when value="paired_interlaced">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	445 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	446 <expand macro="type_paired"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	447 <expand macro="orientation"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	448 </when>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	449 <when value="paired_collection">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	450 <param format="@FORMAT@" name="input" type="data_collection" collection_type="list:paired" label="@LABEL@: collection"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	451 <expand macro="type_paired"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	452 <expand macro="orientation"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	453 </when>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	454 </conditional>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	455 <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the same sample, it means that they belong to the same library.">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	456 <option value="true" selected="true">True</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	457 <option value="false">False</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	458 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	459 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	460
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	461 <xml name="orientation">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	462 <param name="orientation" type="select" label="Select orientation of reads" help="Note: mate-pair fragments are generally in a RF conformation. In general, paired-end reads tend to be in a FR orientation.">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	463 <option value="fr" selected="true"><![CDATA[FR (-> <-)]]></option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	464 <option value="rf"><![CDATA[RF (<- ->)]]></option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	465 <option value="ff"><![CDATA[FF (-> ->)]]></option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	466 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	467 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	468
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	469 <xml name="type_paired">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	470 <param name="type_paired" type="select" label="Type of paired-reads"
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	471 help="In paired-end sequencing, the library preparation yields a set of fragments, and the machine sequences each fragment from both ends. In mate-pair sequencing,
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	472 the library preparation yields two fragments that are distal to each other in the genome and in the opposite in orientation to that of a mate-paired fragment.">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	473 <option value="pe" selected="true">Default (--pe)</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	474 <option value="mp">Mate-pair reads (--mp)</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	475 <option value="hqmp">High-quality Nextera mate-pair reads (--hqmp)</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	476 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	477 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	478
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	479 <xml name="input_additional_files_all" token_format="" token_label="" token_help="">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	480 <conditional name="additional_reads">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	481 <param name="selector" type="select" label="Use an additional set of short-reads" help="Enable this option if you want to combine to data sources (e.g. single and paired reads).">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	482 <option value="false" selected="true">Disabled</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	483 <option value="true">Enabled</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	484 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	485 <when value="true">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	486 <expand macro="input_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	487 <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the sample sample, it means that they belong to the same library.">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	488 <option value="true" selected="true">True</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	489 <option value="false">False</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	490 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	491 </when>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	492 <when value="false"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	493 </conditional>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	494 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	495
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	496 <xml name="input_additional_files_paired" token_format="" token_label="" token_help="" >
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	497 <conditional name="additional_reads">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	498 <param name="selector" type="select" label="Use an additional set of short-reads" help="Enable this option if you want to combine to data sources (e.g. single and paired reads).">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	499 <option value="false" selected="true">Disabled</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	500 <option value="true">Enabled</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	501 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	502 <when value="true">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	503 <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	504 <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the sample sample, it means that they belong to the same library.">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	505 <option value="true" selected="true">True</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	506 <option value="false">False</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	507 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	508 </when>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	509 <when value="false"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	510 </conditional>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	511 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	512
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	513 <xml name="covcutoff">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	514 <conditional name="cov_cond">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	515 <param argument="--cov-cutoff" type="select" label="Set coverage cutoff option" help="When set to 'auto' SPAdes automatically computes coverage threshold using conservative strategy">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	516 <option value="off">Off</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	517 <option value="auto">Auto</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	518 <option value="value">User specific</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	519 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	520 <when value="off"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	521 <when value="auto"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	522 <when value="value">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	523 <param name="manual" type="float" min="0" value="" label="Set value"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	524 </when>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	525 </conditional>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	526 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	527 <xml name="pipeline_options">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	528 <param name="mode_sel" type="select" label="Pipeline options" multiple="true" optional="true" display="checkboxes" help="Error correction requires FASTQ input files.">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	529 <option value="--disable-rr">Disable repeat resolution (--disable-rr)</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	530 <yield/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	531 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	532 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	533 <xml name="kmer" token_help="" token_default="21,33,55,77">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	534 <conditional name="kmer_cond">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	535 <param name="kmer_sel" argument="-k" type="select" label="Select k-mer detection option" help="@HELP@ Comma-separated list, all values must be odd, less than 128 and listed in ascending order.">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	536 <option value="auto">Auto</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	537 <option value="manual">User specific</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	538 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	539 <when value="auto"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	540 <when value="manual">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	541 <param name="manual" type="text" value="@DEFAULT@" label="K-mer size values" help="List of k-mer sizes (must be odd and less than 128)">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	542 <sanitizer invalid_char="">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	543 <valid initial="string.digits">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	544 <add value="," />
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	545 </valid>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	546 </sanitizer>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	547 <validator type="regex">[0-9,]+</validator>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	548 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	549 </when>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	550 </conditional>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	551 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	552 <xml name="nanopore_pacbio">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	553 <param argument="--nanopore" type="data" format="fastq,fastq.gz" multiple="true" optional="true" label="Nanopore reads" help="SPAdes will use Oxford Nanopore reads for gap closure and repeat resolution"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	554 <param argument="--pacbio" type="data" format="fastq,fastq.gz" multiple="true" optional="true" label="PacBio CLR reads" help="It is not recommended to run SPAdes on PacBio reads with low coverage (less than 5). In addition, SPAdes develpers suggest not to run SPAdes on PacBio reads for large genomes. SPAdes will use PacBio CLR reads for gap closure and repeat resolution"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	555 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	556 <xml name="flrna">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	557 <param argument="--fl-rna" name="flrna" type="data" format="fastq,fastq.gz,fasta,fasta.gz,fastqsanger,fastqsanger.gz" multiple="true" optional="true" label="PacBio/Nanopore/contigs that capture full-length transcripts" help="In addition to long reads, you may also provide a separate file with reads capturing the entire transcript sequences using this option. Full-length transcripts in such reads can be typically detected using the adapters. Note, that FL reads should be trimmed so that the adapters are excluded."/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	558 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	559
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	560 <xml name="phred">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	561 <param argument="--phred-offset" type="select" label="Set Phred quality offset" help="Phred quality offset in the input reads. Default: auto-detect">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	562 <option value="auto" selected="true">Auto</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	563 <option value="33">33 (Sanger)</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	564 <option value="64">64 (Illumina)</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	565 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	566 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	567 <xml name="reads" token_paramname="reads" token_help="" token_label="">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	568 <param name="@PARAMNAME@" type="data" format="fastq,fastq.gz" label="@LABEL@ reads" help="@HELP@"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	569 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	570 <xml name="sanger">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	571 <param argument="--sanger" type="data" format="fastq,fastq.gz" multiple="true" optional="true" label="Sanger reads"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	572 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	573 <xml name="contigs">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	574 <param argument="--trusted-contigs" type="data" format="fasta,fasta.gz" multiple="true" optional="true" label="Trusted contigs" help="Reliable contigs of the same genome, which are likely to have no misassemblies and small rate of other errors (e.g. mismatches and indels). This option is not intended for contigs of the related species."/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	575 <param argument="--untrusted-contigs" type="data" format="fasta,fasta.gz" multiple="true" optional="true" label="Untrusted contigs" help="Contigs of the same genome, quality of which is average or unknown. Contigs of poor quality can be used but may introduce errors in the assembly. This option is also not intended for contigs of the related species."/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	576 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	577 <xml name="assembly_graph">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	578 <param argument="--assembly-graph" type="data" format="gfa1" multiple="true" optional="true" label="Assembly graphs" help=" The primary purpose of this option to run these pipelines on already constructed and simplified assembly graph this way skipping a large part of SPAdes pipeline."/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	579 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	580 <xml name="optional_output">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	581 <param name="optional_output" type="select" multiple="true" optional="false" label="Select optional output file(s)" help="Only shown in history if selected here and generated by the specific run.">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	582 <option value="ag" selected="true">Assembly graph</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	583 <option value="ags" selected="true">Assembly graph with scaffolds</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	584 <option value="cn" selected="true">Contigs</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	585 <option value="cp">Contigs paths</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	586 <option value="cr">Corrected reads</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	587 <option value="cs">Contigs stats</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	588 <option value="l">Log</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	589 <option value="sc" selected="true">Scaffolds</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	590 <option value="sp">Scaffolds paths</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	591 <option value="ss">Scaffolds stats</option>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	592 </param>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	593 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	594 <!--
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	595 output
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	596 -->
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	597
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	598 <xml name="out_ag">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	599 <data name="out_ag" format="fastg" from_work_dir="output/assembly_graph.fastg" label="${tool.name} on ${on_string}: Assembly graph">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	600 <filter>'ag' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	601 <filter> operation_mode != '--only-error-correction'</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	602 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	603 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	604 <xml name="out_ags">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	605 <data name="out_ags" format="txt" from_work_dir="output/assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: Assembly graph with scaffolds">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	606 <filter>'ags' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	607 <filter> operation_mode != '--only-error-correction'</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	608 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	609 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	610 <xml name="out_cn">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	611 <data name="out_cn" format="fasta" from_work_dir="output/contigs.fasta" label="${tool.name} on ${on_string}: Contigs">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	612 <filter>'cn' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	613 <filter> operation_mode != '--only-error-correction'</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	614 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	615 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	616 <xml name="out_cp">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	617 <data name="out_cp" format="txt" from_work_dir="output/contigs.paths" label="${tool.name} on ${on_string}: Contigs paths">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	618 <filter>'cp' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	619 <filter> operation_mode != '--only-error-correction'</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	620 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	621 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	622 <xml name="out_cr">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	623 <!-- some mode combinations create fastq, some fasta -->
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	624 <collection name="out_cr" type="list" label="${tool.name} on ${on_string}: Corrected reads">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	625 <filter>'cr' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	626 <filter> operation_mode != '--only-assembler'</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	627 <discover_datasets pattern="(?P<designation>.+)\.fastq\.gz" format="fastq" directory="output/corrected"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	628 <discover_datasets pattern="(?P<designation>.+)\.fasta\.gz" format="fasta" directory="output/corrected"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	629 </collection>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	630 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	631 <xml name="out_cs">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	632 <data name="out_cs" format="tabular" label="${tool.name} on ${on_string}: Contigs stats">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	633 <actions>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	634 <action name="column_names" type="metadata" default="name,length,coverage"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	635 </actions>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	636 <filter>'cs' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	637 <filter> operation_mode != '--only-error-correction'</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	638 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	639 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	640 <xml name="out_l">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	641 <data name="out_l" format="txt" from_work_dir="output/spades.log" label="${tool.name} on ${on_string}: Log">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	642 <filter>'l' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	643 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	644 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	645 <xml name="out_sc">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	646 <data name="out_sc" format="fasta" from_work_dir="output/scaffolds.fasta" label="${tool.name} on ${on_string}: Scaffolds">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	647 <filter>'sc' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	648 <filter> operation_mode != '--only-error-correction'</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	649 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	650 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	651 <xml name="out_sp">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	652 <data name="out_sp" format="txt" from_work_dir="output/scaffolds.paths" label="${tool.name} on ${on_string}: Scaffolds paths">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	653 <filter>'sp' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	654 <filter> operation_mode != '--only-error-correction'</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	655 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	656 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	657 <xml name="out_ss">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	658 <data name="out_ss" format="tabular" label="${tool.name} on ${on_string}: Scaffolds stats">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	659 <actions>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	660 <action name="column_names" type="metadata" default="name,length,coverage"/>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	661 </actions>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	662 <filter>'ss' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	663 <filter> operation_mode != '--only-error-correction'</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	664 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	665 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	666 <xml name="out_rs">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	667 <data name="out_rs" format="fasta" from_work_dir="output/raw_scaffolds.fasta" label="${tool.name} on ${on_string}: Raw scaffolds">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	668 <filter>'rs' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	669 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	670 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	671 <xml name="out_b">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	672 <data name="out_b" format="txt" from_work_dir="output/hmm_statistics.txt" label="${tool.name} on ${on_string}: HMM statistics">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	673 <filter>'b' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	674 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	675 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	676 <xml name="out_dg">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	677 <data name="out_dg" format="fasta" from_work_dir="output/domain_graph.dot" label="${tool.name} on ${on_string}: Domain graph">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	678 <filter>'dg' in optional_output</filter>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	679 </data>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	680 </xml>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	681 <!--
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	682 help
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	683 -->
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	684
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	685 <token name="@HELP_IN@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	686
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	687 SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	688
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	689 To run SPAdes 3.15.3 you need at least one library of the following types:
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	690
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	691 - Illumina paired-end/high-quality mate-pairs/unpaired reads
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	692 - IonTorrent paired-end/high-quality mate-pairs/unpaired reads
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	693 - PacBio CCS reads
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	694 - Illumina and IonTorrent libraries should not be assembled together. All other types of input data are compatible. SPAdes should not be used if only PacBio CLR, Oxford Nanopore, Sanger reads or additional contigs are available.
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	695
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	696 SPAdes supports mate-pair only assembly. However, we recommend to use only high-quality mate-pair libraries in this case (e.g. that do not have a paired-end part). We tested mate-pair only pipeline using Illumina Nextera mate-pairs.
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	697
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	698 Notes:
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	699
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	700 - It is strongly suggested to provide multiple paired-end and mate-pair libraries according to their insert size (from smallest to longest).
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	701 - It is not recommended to run SPAdes on PacBio reads with low coverage (less than 5).
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	702 - We suggest not to run SPAdes on PacBio reads for large genomes.
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	703 - SPAdes accepts gzip-compressed files.
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	704
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	705 A detailed description can be found in the `input section <https://github.com/ablab/spades/#sec3.1>`_ of the manual.
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	706 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	707 <token name="@HELP_OUT_AG@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	708 - Assembly graph
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	709 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	710 <token name="@HELP_OUT_AGS@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	711 - Assembly graph with scaffolds
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	712 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	713 <token name="@HELP_OUT_C@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	714 - Contigs
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	715 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	716 <token name="@HELP_OUT_CP@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	717 - Contigs paths in the assembly graph
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	718 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	719 <token name="@HELP_OUT_CS@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	720 - Contigs stats
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	721 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	722 <token name="@HELP_OUT_CR@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	723 - Corrected reads by BayesHammer
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	724 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	725 <token name="@HELP_OUT_L@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	726 - Log file
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	727 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	728 <token name="@HELP_OUT_S@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	729 - Scaffolds (recommended for use as resulting sequences)
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	730 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	731 <token name="@HELP_OUT_SP@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	732 - Scaffolds paths in the assembly graph
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	733 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	734 <token name="@HELP_OUT_SS@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	735 - Scaffolds stats
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	736 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	737 <token name="@HELP_WID@">
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	738 SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	739 </token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	740 <token name="@IONTORRENT@"><![CDATA[
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	741 The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our `recommendation for long reads <https://cab.spbu.ru/files/release3.12.0/manual.html#sec3.4>`_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <previous_output_dir>. Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	742
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	743 You may need no error correction for Hi-Q enzyme at all. However, we suggest trying to assemble your data with and without error correction and select the best variant.
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	744
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	745 For non-trivial datasets (e.g. with high GC, low or uneven coverage) we suggest to enable single-cell mode (setting --sc option) and use k-mer lengths of 21,33,55.
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	746
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	747 ]]></token>
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	748
42a39792aaae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813" iuc parents: diff changeset	749 </macros>

Mercurial > repos > iuc > spades_biosyntheticspades

annotate macros.xml @ 0:42a39792aaae draft