stacks_procrad: stacks_procrad.xml annotate

annotate stacks_procrad.xml @ 9:390aab905bc2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb

author	iuc
date	Fri, 07 Apr 2023 21:53:46 +0000
parents	93df40cf4d4b
children

rev	line source
1 a67dae0b1327 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f iuc parents: 0 diff changeset	1 <tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.0">
8 93df40cf4d4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139" iuc parents: 6 diff changeset	2 <description>the Stacks demultiplexing script</description>
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	3 <macros>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	4 <import>macros.xml</import>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	5 </macros>
9 390aab905bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb iuc parents: 8 diff changeset	6 <expand macro="bio_tools"/>
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	7 <expand macro="requirements"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	8 <expand macro="stdio"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	9 <command><![CDATA[
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	10
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	11 #if $input_type.options_type_selector == "single"
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	12
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	13 #if $input_type.input_single.is_of_type('fastqsanger')
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	14 #set $ext = ".fq"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	15 #set inputype = "fastq"
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	16 #else
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	17 #set $ext = ".fq.gz"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	18 #set inputype = "gzfastq"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	19 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	20
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	21 ln -s '$input_type.input_single' R1$ext &&
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	22 #else
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	23
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	24 #if $input_type.inputs_paired1.is_of_type('fastqsanger')
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	25 #set $ext = ".fq"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	26 #set inputype = "fastq"
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	27 #else
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	28 #set $ext = ".fq.gz"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	29 #set inputype = "gzfastq"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	30 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	31
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	32 ln -s '$input_type.inputs_paired1' R1$ext &&
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	33 ln -s '$input_type.inputs_paired2' R2$ext &&
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	34 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	35
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	36 mkdir stacks_outputs
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	37
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	38 &&
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	39
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	40 process_radtags
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	41
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	42 #if $input_type.options_type_selector == "single"
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	43 -f R1$ext
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	44 #else
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	45 -1 R1$ext
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	46 -2 R2$ext
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	47 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	48
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	49 -i $inputype
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	50 -b '$barcode'
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	51
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	52 $input_type.barcode_encoding
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	53
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	54 #if str( $options_enzyme.options_enzyme_selector ) == "1"
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	55 -e $options_enzyme.enzyme
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	56 #else
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	57 --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	58 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	59
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	60 #if str( $outype ) != "auto"
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	61 -y $outype
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	62 #end if
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	63
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	64 $capture
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	65
3 ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	66 $options_advanced.retain_header
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	67
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	68 #if str($options_advanced.truncate)
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	69 -t $options_advanced.truncate
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	70 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	71
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	72 -w $options_advanced.sliding
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	73
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	74 $options_advanced.remove
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	75
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	76 $options_advanced.discard
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	77 -s $options_advanced.score
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	78
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	79 $options_advanced.rescue
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	80
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	81 -o stacks_outputs
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	82 ]]></command>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	83
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	84 <inputs>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	85 <conditional name="input_type">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	86 <param name="options_type_selector" type="select" label="Single-end or paired-end reads files">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	87 <option value="single" selected="True">Single-end files</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	88 <option value="paired">Paired-end files</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	89 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	90 <when value="single">
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	91 <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" />
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	92
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	93 <param name="barcode_encoding" type="select" label="Barcode location">
6 0750175d6a7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: 5 diff changeset	94 <expand macro="barcode_encoding_single" />
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	95 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	96 </when>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	97 <when value="paired">
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	98 <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" />
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	99 <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 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	100
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	101 <param name="barcode_encoding" type="select" label="Barcode location">
6 0750175d6a7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439 iuc parents: 5 diff changeset	102 <expand macro="barcode_encoding_pair" />
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	103 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	104 </when>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	105 </conditional>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	106
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	107 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" help="Barcode file" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	108
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	109 <conditional name="options_enzyme">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	110 <param name="options_enzyme_selector" type="select" label="Number of enzymes">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	111 <option value="1">One</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	112 <option value="2">Two</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	113 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	114 <when value="1">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	115 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" >
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	116 <expand macro="enzymes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	117 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	118 </when>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	119 <when value="2">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	120 <param name="enzyme" type="select" label="Enzyme" argument="--renz_1" help="provide the restriction enzyme used" >
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	121 <expand macro="enzymes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	122 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	123 <param name="enzyme2" type="select" label="Second enzyme" argument="--renz_2" help="provide the second restriction enzyme used" >
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	124 <expand macro="enzymes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	125 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	126 </when>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	127 </conditional>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	128
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	129 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	130
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	131 <section name="options_advanced" title="advanced options" expanded="False">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	132 <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)" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	133 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	134 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	135 <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)" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	136 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	137 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
9 390aab905bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb iuc parents: 8 diff changeset	138 <param type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" />
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	139 </section>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	140
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	141 <param name="outype" argument="-y" type="select" label="Output format" >
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	142 <option value="auto" selected="True">Same as input</option>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	143 <option value="fastq">fastq</option>
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	144 <option value="fasta">fasta</option>
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	145 <option value="gzfastq">gzipped fastq</option>
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	146 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	147 </inputs>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	148
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	149 <outputs>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	150 <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" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	151
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	152 <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	153 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	154 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	155 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	156 </collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	157 <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	158 <filter>input_type['options_type_selector'] == "paired"</filter>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	159 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	160 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	161 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	162 </collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	163 <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	164 <filter>capture is True</filter>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	165 <discover_datasets pattern="(?P<name>.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" />
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	166 <discover_datasets pattern="(?P<name>.+)\.fq\.gz.discards$" ext="fastqsanger" directory="stacks_outputs" /> <!-- discards are never gzipped -->
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	167 <discover_datasets pattern="(?P<name>.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	168 </collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	169 </outputs>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	170
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	171 <tests>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	172 <test>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	173 <param name="options_type_selector" value="single"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	174 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	175 <param name="barcode" value="procrad/barcodes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	176 <param name="options_enzyme_selector" value="1"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	177 <param name="enzyme" value="ecoRI"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	178 <param name="discard" value="true"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	179 <param name="capture" value="true"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	180 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	181 <output_collection name="demultiplexed">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	182 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	183 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	184 <output_collection name="discarded">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	185 <element name="R1">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	186 <assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	187 <has_text text="lane1_fakedata0_11" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	188 </assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	189 </element>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	190 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	191 </test>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	192 <test>
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	193 <param name="options_type_selector" value="single"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	194 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	195 <param name="barcode" value="procrad/barcodes"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	196 <param name="options_enzyme_selector" value="1"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	197 <param name="enzyme" value="ecoRI"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	198 <param name="discard" value="true"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	199 <param name="capture" value="true"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	200 <param name="outype" value="gzfastq"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	201 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	202 <output_collection name="demultiplexed">
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	203 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	204 </output_collection>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	205 <output_collection name="discarded">
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	206 <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	207 </output_collection>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	208 </test>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	209 <test>
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	210 <param name="options_type_selector" value="paired"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	211 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	212 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	213 <param name="barcode" value="procrad/barcodes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	214 <param name="options_enzyme_selector" value="1"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	215 <param name="enzyme" value="ecoRI"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	216 <param name="discard" value="true"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	217 <param name="capture" value="true"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	218 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	219 <output_collection name="demultiplexed">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	220 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	221 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	222 <output_collection name="remaining">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	223 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	224 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	225 <output_collection name="discarded">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	226 <element name="R1">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	227 <assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	228 <has_text text="lane1_fakedata0_11" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	229 </assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	230 </element>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	231 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	232 </test>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	233 <test>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	234 <param name="options_type_selector" value="paired"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	235 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	236 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	237 <param name="barcode" value="procrad/barcodes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	238 <param name="options_enzyme_selector" value="1"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	239 <param name="enzyme" value="ecoRI"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	240 <param name="discard" value="true"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	241 <param name="capture" value="true"/>
3 ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	242 <param name="retain_header" value="true"/>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	243 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	244 <output_collection name="demultiplexed">
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	245 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fq.header"/>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	246 </output_collection>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	247 <output_collection name="remaining">
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	248 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fq"/>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	249 </output_collection>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	250 <output_collection name="discarded">
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	251 <element name="R1">
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	252 <assert_contents>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	253 <has_text text="lane1_fakedata0_11" />
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	254 </assert_contents>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	255 </element>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	256 </output_collection>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	257 </test>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	258 <test>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	259 <param name="options_type_selector" value="paired"/>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	260 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	261 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	262 <param name="barcode" value="procrad/barcodes"/>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	263 <param name="options_enzyme_selector" value="1"/>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	264 <param name="enzyme" value="ecoRI"/>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	265 <param name="discard" value="true"/>
ba12012b4984 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 1 diff changeset	266 <param name="capture" value="true"/>
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	267 <param name="outype" value="fasta"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	268 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	269 <output_collection name="demultiplexed">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	270 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fa"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	271 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	272 <output_collection name="remaining">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	273 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fa"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	274 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	275 <output_collection name="discarded">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	276 <element name="R1">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	277 <assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	278 <has_text text="lane1_fakedata0_11" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	279 </assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	280 </element>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	281 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	282 </test>
5 faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	283 <test>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	284 <param name="options_type_selector" value="single"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	285 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq.gzip"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	286 <param name="barcode" value="procrad/barcodes"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	287 <param name="options_enzyme_selector" value="1"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	288 <param name="enzyme" value="ecoRI"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	289 <param name="discard" value="true"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	290 <param name="capture" value="true"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	291 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	292 <output_collection name="demultiplexed">
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	293 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	294 </output_collection>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	295 <output_collection name="discarded">
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	296 <element name="R1">
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	297 <assert_contents>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	298 <has_text text="lane1_fakedata0_11" />
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	299 </assert_contents>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	300 </element>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	301 </output_collection>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	302 </test>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	303 <test>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	304 <param name="options_type_selector" value="single"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	305 <param name="input_single" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	306 <param name="barcode" value="procrad/barcodes"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	307 <param name="options_enzyme_selector" value="1"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	308 <param name="enzyme" value="ecoRI"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	309 <param name="discard" value="true"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	310 <param name="capture" value="true"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	311 <param name="outype" value="gzfastq"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	312 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	313 <output_collection name="demultiplexed">
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	314 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq.gzip"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	315 </output_collection>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	316 <output_collection name="discarded">
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	317 <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	318 </output_collection>
faa96a21f8e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 3 diff changeset	319 </test>
0 1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	320 </tests>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	321
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	322
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	323
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	324 <help>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	325 <![CDATA[
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	326 .. class:: infomark
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	327
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	328 What it does
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	329
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	330 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).
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	331
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	332 The process_radtags program can:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	333
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	334 - handle data that is barcoded, either inline or using an index, or unbarcoded.
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	335 - use combinatorial barcodes.
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	336 - check and correct for a restriction enzyme cutsite for single or double-digested data.
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	337 - filter adapter sequence while allowing for sequencing error in the adapter pattern.
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	338 - process individual files or whole directories of files.
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	339 - directly read gzipped data
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	340 - filter reads based on Illumina's Chastity filter
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	341
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	342 Help
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	343
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	344 Input files:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	345
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	346 - FASTQ
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	347
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	348 - Barcode File Format
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	349
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	350 The barcode file is a very simple format:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	351
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	352 ======= ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	353 Barcode Sample name
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	354 ======= ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	355 ATGGGG PopA_01
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	356 GGGTAA PopA_02
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	357 AGGAAA PopA_03
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	358 TTTAAG PopA_04
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	359 GGTGTG PopA_05
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	360 TGATGT PopA_06
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	361 ======= ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	362
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	363 Combinatorial barcodes are specified, one per column, separated by a tab:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	364
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	365 ======== ======== ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	366 Barcode1 Barcode2 Sample name
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	367 ======== ======== ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	368 CGATA ACGTA PopA_01
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	369 CGGCG CGTA PopA_02
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	370 GAAGC CGTA PopA_03
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	371 GAGAT CGTA PopA_04
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	372 CGATA AGCA PopA_05
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	373 CGGCG AGCA PopA_06
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	374 ======== ======== ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	375
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	376 @STACKS_INFOS@
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	377 ]]>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	378 </help>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	379 <expand macro="citation" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: diff changeset	380 </tool>

Mercurial > repos > iuc > stacks_procrad

annotate stacks_procrad.xml @ 9:390aab905bc2 draft default tip