stacks_procrad: stacks_procrad.xml annotate

annotate stacks_procrad.xml @ 12:eded025438db 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 22:00:56 +0000
parents	be78e39d56b3
children

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">
11 be78e39d56b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139" iuc parents: 9 diff changeset	2 <description>the Stacks demultiplexing script</description>
0 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>
12 eded025438db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb iuc parents: 11 diff changeset	6 <expand macro="bio_tools"/>
0 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="requirements"/>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	8 <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	9 <command><![CDATA[
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	10
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	11 #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	12
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	13 #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	14 #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	15 #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	16 #else
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	17 #set $ext = ".fq.gz"
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	18 #set inputype = "gzfastq"
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	19 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	20
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	21 ln -s '$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	22 #else
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	23
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	24 #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	25 #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	26 #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	27 #else
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	28 #set $ext = ".fq.gz"
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	29 #set inputype = "gzfastq"
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	30 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	31
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	32 ln -s '$input_type.inputs_paired1' R1$ext &&
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	33 ln -s '$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	34 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	35
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	36 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	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
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	40 process_radtags
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	41
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	42 #if $input_type.options_type_selector == "single"
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	43 -f R1$ext
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	44 #else
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	45 -1 R1$ext
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	46 -2 R2$ext
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	47 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	48
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	49 -i $inputype
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	50 -b '$barcode'
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	51
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	52 $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	53
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	54 #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	55 -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	56 #else
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	57 --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	58 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	59
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	60 #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	61 -y $outype
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	62 #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	63
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	64 $capture
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	65
6 2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	66 $options_advanced.retain_header
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	67
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	68 #if str($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	69 -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	70 #end if
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	71
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	72 -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	73
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	74 $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	75
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	76 $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	77 -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	78
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	79 $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	80
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	81 -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	82 ]]></command>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	83
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	84 <inputs>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	85 <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	86 <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	87 <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	88 <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	89 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	90 <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	91 <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	92
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	93 <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	94 <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	95 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	96 </when>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	97 <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	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" />
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 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 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	100
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	101 <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	102 <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	103 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	104 </when>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	105 </conditional>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	106
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	107 <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	108
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	109 <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	110 <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	111 <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	112 <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	113 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	114 <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	115 <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	116 <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	117 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	118 </when>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	119 <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	120 <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	121 <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	122 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	123 <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	124 <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	125 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	126 </when>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	127 </conditional>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	128
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	129 <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	130
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	131 <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	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)" />
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="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	134 <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	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)" />
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="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	137 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
12 eded025438db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb iuc parents: 11 diff changeset	138 <param 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	139 </section>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	140
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	141 <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	142 <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	143 <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	144 <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	145 <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	146 </param>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	147 </inputs>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	148
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	149 <outputs>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty 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" />
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	151
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	152 <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}">
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	153 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq$" 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	154 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	155 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fa$" 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	156 </collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	157 <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	158 <filter>input_type['options_type_selector'] == "paired"</filter>
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	159 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq$" 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	160 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" />
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	161 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fa$" 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	162 </collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	163 <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}">
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	164 <filter>capture is True</filter>
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	165 <discover_datasets pattern="(?P<name>.+)\.fq\.discards$" 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	166 <discover_datasets pattern="(?P<name>.+)\.fq\.gz.discards$" ext="fastqsanger" directory="stacks_outputs" /> <!-- discards are never gzipped -->
3 11642e18f2b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	167 <discover_datasets pattern="(?P<name>.+)\.fa\.discards$" 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	168 </collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	169 </outputs>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	170
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	171 <tests>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	172 <test>
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="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	174 <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	175 <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	176 <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	177 <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	178 <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	179 <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	180 <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	181 <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	182 <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	183 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	184 <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	185 <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	186 <assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	187 <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	188 </assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	189 </element>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	190 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	191 </test>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	192 <test>
8 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="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	194 <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	195 <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	196 <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	197 <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	198 <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	199 <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	200 <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	201 <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	202 <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	203 <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	204 </output_collection>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	205 <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	206 <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	207 </output_collection>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	208 </test>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	209 <test>
0 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="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	211 <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	212 <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	213 <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	214 <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	215 <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	216 <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	217 <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	218 <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	219 <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	220 <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	221 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	222 <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	223 <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	224 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	225 <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	226 <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	227 <assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	228 <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	229 </assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	230 </element>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	231 </output_collection>
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 <test>
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="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	235 <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	236 <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	237 <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	238 <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	239 <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	240 <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	241 <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	242 <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	243 <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	244 <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	245 <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	246 </output_collection>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	247 <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	248 <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	249 </output_collection>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	250 <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	251 <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	252 <assert_contents>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	253 <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	254 </assert_contents>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	255 </element>
2837e6ae4e18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78 iuc parents: 4 diff changeset	256 </output_collection>
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 <test>
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="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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 <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	267 <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	268 <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	269 <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	270 <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	271 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	272 <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	273 <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	274 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	275 <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	276 <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	277 <assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	278 <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	279 </assert_contents>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	280 </element>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	281 </output_collection>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	282 </test>
8 bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	283 <test>
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="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	285 <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	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 </output_collection>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	295 <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	296 <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	297 <assert_contents>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	298 <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	299 </assert_contents>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	300 </element>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	301 </output_collection>
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 <test>
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="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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 <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	314 <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	315 </output_collection>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	316 <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	317 <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	318 </output_collection>
bec1f08cdfcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e iuc parents: 6 diff changeset	319 </test>
0 6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	320 </tests>
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
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	324 <help>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	325 <![CDATA[
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	326 .. class:: infomark
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	327
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	328 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	329
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty 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).
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	331
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	332 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	333
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	334 - 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	335 - 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	336 - 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	337 - 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	338 - 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	339 - 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	340 - 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	341
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	342 Help
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	343
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	344 Input files:
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	345
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	346 - FASTQ
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	347
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	348 - 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	349
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	350 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	351
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	352 ======= ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	353 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	354 ======= ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	355 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	356 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	357 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	358 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	359 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	360 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	361 ======= ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	362
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	363 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	364
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	365 ======== ======== ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	366 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	367 ======== ======== ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	368 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	369 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	370 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	371 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	372 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	373 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	374 ======== ======== ===========
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	375
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	376 @STACKS_INFOS@
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	377 ]]>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	378 </help>
6f9e8593e571 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	379 <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	380 </tool>

Mercurial > repos > iuc > stacks_procrad

annotate stacks_procrad.xml @ 12:eded025438db draft default tip