stacks_procrad: stacks_procrad.xml annotate

annotate stacks_procrad.xml @ 9:57910d476be9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439

author	iuc
date	Sun, 21 May 2017 18:52:17 -0400
parents	bec1f08cdfcc
children	be78e39d56b3

rev	line source
4 c2733bcc51f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f iuc parents: 3 diff changeset	1 <tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.0">
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	2 <description>the Stacks demultiplexing script</description>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	3 <macros>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	4 <import>macros.xml</import>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	5 </macros>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	6 <expand macro="requirements"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	7 <expand macro="stdio"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	8 <command><![CDATA[
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	9
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	10 #if $input_type.options_type_selector == "single"
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	11
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	12 #if $input_type.input_single.is_of_type('fastqsanger')
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	13 #set $ext = ".fq"
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	14 #set inputype = "fastq"
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	15 #else
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	16 #set $ext = ".fq.gz"
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	17 #set inputype = "gzfastq"
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	18 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	19
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	20 ln -s '$input_type.input_single' R1$ext &&
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	21 #else
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	22
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	23 #if $input_type.inputs_paired1.is_of_type('fastqsanger')
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	24 #set $ext = ".fq"
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	25 #set inputype = "fastq"
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	26 #else
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	27 #set $ext = ".fq.gz"
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	28 #set inputype = "gzfastq"
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	29 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	30
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	31 ln -s '$input_type.inputs_paired1' R1$ext &&
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	32 ln -s '$input_type.inputs_paired2' R2$ext &&
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	33 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	34
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	35 mkdir stacks_outputs
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	36
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	37 &&
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	38
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	39 process_radtags
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	40
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	41 #if $input_type.options_type_selector == "single"
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	42 -f R1$ext
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	43 #else
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	44 -1 R1$ext
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	45 -2 R2$ext
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	46 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	47
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	48 -i $inputype
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	49 -b '$barcode'
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	50
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	51 $input_type.barcode_encoding
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	52
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	53 #if str( $options_enzyme.options_enzyme_selector ) == "1"
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	54 -e $options_enzyme.enzyme
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	55 #else
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	56 --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	57 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	58
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	59 #if str( $outype ) != "auto"
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	60 -y $outype
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	61 #end if
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	62
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	63 $capture
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	64
6 2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	65 $options_advanced.retain_header
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	66
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	67 #if str($options_advanced.truncate)
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	68 -t $options_advanced.truncate
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	69 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	70
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	71 -w $options_advanced.sliding
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	72
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	73 $options_advanced.remove
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	74
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	75 $options_advanced.discard
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	76 -s $options_advanced.score
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	77
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	78 $options_advanced.rescue
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	79
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	80 -o stacks_outputs
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	81 ]]></command>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	82
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	83 <inputs>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	84 <conditional name="input_type">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	85 <param name="options_type_selector" type="select" label="Single-end or paired-end reads files">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	86 <option value="single" selected="True">Single-end files</option>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	87 <option value="paired">Paired-end files</option>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	88 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	89 <when value="single">
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	90 <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" />
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	91
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	92 <param name="barcode_encoding" type="select" label="Barcode location">
9 57910d476be9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: 8 diff changeset	93 <expand macro="barcode_encoding_single" />
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	94 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	95 </when>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	96 <when value="paired">
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	97 <param name="inputs_paired1" argument="-1" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" />
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	98 <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" />
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	99
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	100 <param name="barcode_encoding" type="select" label="Barcode location">
9 57910d476be9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: 8 diff changeset	101 <expand macro="barcode_encoding_pair" />
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	102 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	103 </when>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	104 </conditional>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	105
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	106 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" help="Barcode file" />
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	107
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	108 <conditional name="options_enzyme">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	109 <param name="options_enzyme_selector" type="select" label="Number of enzymes">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	110 <option value="1">One</option>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	111 <option value="2">Two</option>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	112 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	113 <when value="1">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	114 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" >
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	115 <expand macro="enzymes"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	116 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	117 </when>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	118 <when value="2">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	119 <param name="enzyme" type="select" label="Enzyme" argument="--renz_1" help="provide the restriction enzyme used" >
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	120 <expand macro="enzymes"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	121 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	122 <param name="enzyme2" type="select" label="Second enzyme" argument="--renz_2" help="provide the second restriction enzyme used" >
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	123 <expand macro="enzymes"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	124 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	125 </when>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	126 </conditional>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	127
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	128 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	129
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	130 <section name="options_advanced" title="advanced options" expanded="False">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	131 <param name="sliding" type="float" value="0.15" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15)" />
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	132 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" />
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	133 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	134 <param name="score" type="integer" value="10" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10)" />
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	135 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	136 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
6 2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	137 <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" />
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	138 </section>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	139
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	140 <param name="outype" argument="-y" type="select" label="Output format" >
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	141 <option value="auto" selected="True">Same as input</option>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	142 <option value="fastq">fastq</option>
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	143 <option value="fasta">fasta</option>
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	144 <option value="gzfastq">gzipped fastq</option>
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	145 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	146 </inputs>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	147
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	148 <outputs>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	149 <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" />
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	150
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	151 <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}">
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	152 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	153 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	154 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	155 </collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	156 <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	157 <filter>input_type['options_type_selector'] == "paired"</filter>
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	158 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	159 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	160 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	161 </collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	162 <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	163 <filter>capture is True</filter>
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	164 <discover_datasets pattern="(?P<name>.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" />
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	165 <discover_datasets pattern="(?P<name>.+)\.fq\.gz.discards$" ext="fastqsanger" directory="stacks_outputs" /> <!-- discards are never gzipped -->
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	166 <discover_datasets pattern="(?P<name>.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" />
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	167 </collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	168 </outputs>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	169
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	170 <tests>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	171 <test>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	172 <param name="options_type_selector" value="single"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	173 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	174 <param name="barcode" value="procrad/barcodes"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	175 <param name="options_enzyme_selector" value="1"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	176 <param name="enzyme" value="ecoRI"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	177 <param name="discard" value="true"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	178 <param name="capture" value="true"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	179 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	180 <output_collection name="demultiplexed">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	181 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	182 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	183 <output_collection name="discarded">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	184 <element name="R1">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	185 <assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	186 <has_text text="lane1_fakedata0_11" />
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	187 </assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	188 </element>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	189 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	190 </test>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	191 <test>
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	192 <param name="options_type_selector" value="single"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	193 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	194 <param name="barcode" value="procrad/barcodes"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	195 <param name="options_enzyme_selector" value="1"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	196 <param name="enzyme" value="ecoRI"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	197 <param name="discard" value="true"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	198 <param name="capture" value="true"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	199 <param name="outype" value="gzfastq"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	200 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	201 <output_collection name="demultiplexed">
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	202 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	203 </output_collection>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	204 <output_collection name="discarded">
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	205 <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	206 </output_collection>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	207 </test>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	208 <test>
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	209 <param name="options_type_selector" value="paired"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	210 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	211 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	212 <param name="barcode" value="procrad/barcodes"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	213 <param name="options_enzyme_selector" value="1"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	214 <param name="enzyme" value="ecoRI"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	215 <param name="discard" value="true"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	216 <param name="capture" value="true"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	217 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	218 <output_collection name="demultiplexed">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	219 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	220 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	221 <output_collection name="remaining">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	222 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fq"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	223 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	224 <output_collection name="discarded">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	225 <element name="R1">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	226 <assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	227 <has_text text="lane1_fakedata0_11" />
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	228 </assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	229 </element>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	230 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	231 </test>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	232 <test>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	233 <param name="options_type_selector" value="paired"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	234 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	235 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	236 <param name="barcode" value="procrad/barcodes"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	237 <param name="options_enzyme_selector" value="1"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	238 <param name="enzyme" value="ecoRI"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	239 <param name="discard" value="true"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	240 <param name="capture" value="true"/>
6 2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	241 <param name="retain_header" value="true"/>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	242 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	243 <output_collection name="demultiplexed">
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	244 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fq.header"/>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	245 </output_collection>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	246 <output_collection name="remaining">
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	247 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fq"/>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	248 </output_collection>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	249 <output_collection name="discarded">
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	250 <element name="R1">
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	251 <assert_contents>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	252 <has_text text="lane1_fakedata0_11" />
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	253 </assert_contents>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	254 </element>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	255 </output_collection>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	256 </test>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	257 <test>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	258 <param name="options_type_selector" value="paired"/>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	259 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	260 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	261 <param name="barcode" value="procrad/barcodes"/>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	262 <param name="options_enzyme_selector" value="1"/>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	263 <param name="enzyme" value="ecoRI"/>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	264 <param name="discard" value="true"/>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	265 <param name="capture" value="true"/>
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	266 <param name="outype" value="fasta"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	267 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	268 <output_collection name="demultiplexed">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	269 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fa"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	270 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	271 <output_collection name="remaining">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	272 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fa"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	273 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	274 <output_collection name="discarded">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	275 <element name="R1">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	276 <assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	277 <has_text text="lane1_fakedata0_11" />
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	278 </assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	279 </element>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	280 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	281 </test>
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	282 <test>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	283 <param name="options_type_selector" value="single"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	284 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq.gzip"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	285 <param name="barcode" value="procrad/barcodes"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	286 <param name="options_enzyme_selector" value="1"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	287 <param name="enzyme" value="ecoRI"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	288 <param name="discard" value="true"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	289 <param name="capture" value="true"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	290 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	291 <output_collection name="demultiplexed">
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	292 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	293 </output_collection>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	294 <output_collection name="discarded">
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	295 <element name="R1">
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	296 <assert_contents>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	297 <has_text text="lane1_fakedata0_11" />
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	298 </assert_contents>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	299 </element>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	300 </output_collection>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	301 </test>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	302 <test>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	303 <param name="options_type_selector" value="single"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	304 <param name="input_single" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	305 <param name="barcode" value="procrad/barcodes"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	306 <param name="options_enzyme_selector" value="1"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	307 <param name="enzyme" value="ecoRI"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	308 <param name="discard" value="true"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	309 <param name="capture" value="true"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	310 <param name="outype" value="gzfastq"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	311 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	312 <output_collection name="demultiplexed">
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	313 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq.gzip"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	314 </output_collection>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	315 <output_collection name="discarded">
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	316 <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	317 </output_collection>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	318 </test>
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	319 </tests>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	320
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	321
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	322
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	323 <help>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	324 <![CDATA[
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	325 .. class:: infomark
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	326
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	327 What it does
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	328
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	329 This program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. This allows for some seqeuncing errors while elimating reads where the sequence is degrading as it is being sequenced. By default the sliding window is 15% of the length of the read, but can be specified on the command line (the threshold and window size can be adjusted).
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	330
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	331 The process_radtags program can:
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	332
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	333 - handle data that is barcoded, either inline or using an index, or unbarcoded.
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	334 - use combinatorial barcodes.
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	335 - check and correct for a restriction enzyme cutsite for single or double-digested data.
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	336 - filter adapter sequence while allowing for sequencing error in the adapter pattern.
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	337 - process individual files or whole directories of files.
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	338 - directly read gzipped data
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	339 - filter reads based on Illumina's Chastity filter
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	340
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	341 Help
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	342
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	343 Input files:
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	344
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	345 - FASTQ
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	346
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	347 - Barcode File Format
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	348
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	349 The barcode file is a very simple format:
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	350
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	351 ======= ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	352 Barcode Sample name
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	353 ======= ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	354 ATGGGG PopA_01
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	355 GGGTAA PopA_02
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	356 AGGAAA PopA_03
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	357 TTTAAG PopA_04
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	358 GGTGTG PopA_05
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	359 TGATGT PopA_06
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	360 ======= ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	361
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	362 Combinatorial barcodes are specified, one per column, separated by a tab:
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	363
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	364 ======== ======== ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	365 Barcode1 Barcode2 Sample name
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	366 ======== ======== ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	367 CGATA ACGTA PopA_01
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	368 CGGCG CGTA PopA_02
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	369 GAAGC CGTA PopA_03
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	370 GAGAT CGTA PopA_04
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	371 CGATA AGCA PopA_05
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	372 CGGCG AGCA PopA_06
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	373 ======== ======== ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	374
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	375 @STACKS_INFOS@
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	376 ]]>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	377 </help>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	378 <expand macro="citation" />
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	379 </tool>

Mercurial > repos > iuc > stacks_procrad

annotate stacks_procrad.xml @ 9:57910d476be9 draft