stacks_denovomap: stacks_denovomap.xml annotate

annotate stacks_denovomap.xml @ 4:998dfec32bde draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f

author	iuc
date	Mon, 26 Sep 2016 11:44:20 -0400
parents	bab631cc9f64
children	34000c653ae5

rev	line source
4 998dfec32bde 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_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.0">
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	2 <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	3 <macros>
9d588fb2aee5 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>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	5 </macros>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	6 <expand macro="requirements"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	7 <expand macro="stdio"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	8 <command><![CDATA[
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	9 #from os.path import splitext
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	10 #import re
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	11
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	12 #if str( $options_usage.rad_analysis_type ) == "genetic":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	13 #for $input_parent in $options_usage.parent_sequences:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	14
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	15 #if $input_parent.ext == "fastqsanger":
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	16 #set $data_path = splitext($input_parent.element_identifier)[0]
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	17 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	18 #set $data_path = $data_path + ".fq"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	19 #else:
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	20 #set $data_path = splitext($input_parent.element_identifier)[0]
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	21 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	22 #set $data_path = $data_path + ".fa"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	23 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	24
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	25 ln -s "${input_parent}" "${data_path}" &&
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	26 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	27
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	28 #for $input_progeny in $options_usage.progeny_sequences:
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	29 #if $input_progeny:
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	30 #if $input_progeny.ext == "fastqsanger":
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	31 #set $data_path = splitext($input_progeny.element_identifier)[0]
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	32 #set $data_path = re.sub(r'\.1$', '', $data_path)
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	33 #set $data_path = $data_path + ".fq"
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	34 #else:
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	35 #set $data_path = splitext($input_progeny.element_identifier)[0]
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	36 #set $data_path = re.sub(r'\.1$', '', $data_path)
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	37 #set $data_path = $data_path + ".fa"
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	38 #end if
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	39
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	40 ln -s "${input_progeny}" "${data_path}" &&
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	41 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	42 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	43 #else:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	44 #for $input_indiv in $options_usage.individual_sample:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	45
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	46 #if $input_indiv.ext == "fastqsanger":
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	47 #set $data_path = splitext($input_indiv.element_identifier)[0]
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	48 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	49 #set $data_path = $data_path + ".fq"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	50 #else:
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	51 #set $data_path = splitext($input_indiv.element_identifier)[0]
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	52 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	53 #set $data_path = $data_path + ".fa"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	54 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	55
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	56 ln -s "${input_indiv}" "${data_path}" &&
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	57 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	58 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	59
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	60 mkdir stacks_outputs
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	61
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	62 &&
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	63
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	64 denovo_map.pl
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	65
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	66 -T \${GALAXY_SLOTS:-1}
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	67
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	68 #if str( $options_usage.rad_analysis_type ) == "genetic":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	69 #for $input_parent in $options_usage.parent_sequences:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	70 #if $input_parent.ext == "fastqsanger":
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	71 #set $data_path = splitext($input_parent.element_identifier)[0]
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	72 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	73 #set $data_path = $data_path + ".fq"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	74 #else:
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	75 #set $data_path = splitext($input_parent.element_identifier)[0]
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	76 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	77 #set $data_path = $data_path + ".fa"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	78 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	79
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	80 -p "${data_path}"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	81 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	82
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	83 -A $options_usage.cross_type
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	84
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	85 #for $input_progeny in $options_usage.progeny_sequences:
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	86 #if $input_progeny:
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	87 #if $input_progeny.ext == "fastqsanger":
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	88 #set $data_path = splitext($input_progeny.element_identifier)[0]
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	89 #set $data_path = re.sub(r'\.1$', '', $data_path)
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	90 #set $data_path = $data_path + ".fq"
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	91 #else:
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	92 #set $data_path = splitext($input_progeny.element_identifier)[0]
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	93 #set $data_path = re.sub(r'\.1$', '', $data_path)
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	94 #set $data_path = $data_path + ".fa"
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	95 #end if
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	96
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	97 -r "${data_path}"
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	98 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	99 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	100
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	101 #if str($assembly_options.P):
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	102 -P $assembly_options.P
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	103 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	104 #else:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	105 #for $i_indiv, $input_indiv in enumerate($options_usage.individual_sample):
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	106
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	107 #if $input_indiv.ext == "fastqsanger":
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	108 #set $data_path = splitext($input_indiv.element_identifier)[0]
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	109 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	110 #set $data_path = $data_path + ".fq"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	111 #else:
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	112 #set $data_path = splitext($input_indiv.element_identifier)[0]
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	113 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	114 #set $data_path = $data_path + ".fa"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	115 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	116
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	117 -s "${data_path}"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	118 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	119 -O "$options_usage.popmap"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	120 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	121
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	122 #if str($assembly_options.m):
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	123 -m $assembly_options.m
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	124 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	125 #if str($assembly_options.N):
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	126 -N $assembly_options.N
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	127 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	128 -M $assembly_options.M
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	129 -n $assembly_options.n
4 998dfec32bde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f iuc parents: 3 diff changeset	130 $assembly_options.t
998dfec32bde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f iuc parents: 3 diff changeset	131 $assembly_options.H
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	132
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	133 ## Batch description
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	134 -b 1
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	135
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	136 ## No SQL recording
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	137 -S
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	138
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	139 ## snp_model
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	140 #if str( $snp_options.select_model.model_type) == "bounded":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	141 --bound_low $snp_options.select_model.bound_low
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	142 --bound_high $snp_options.select_model.bound_high
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	143 --alpha $snp_options.select_model.alpha
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	144 #else if str( $snp_options.select_model.model_type) == "snp":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	145 --alpha $snp_options.select_model.alpha
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	146 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	147
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	148 -o stacks_outputs
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	149
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	150 #if str( $options_usage.rad_analysis_type ) == "genetic":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	151 @NORM_GENOTYPES_OUTPUT_LIGHT@
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	152 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	153 ]]></command>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	154
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	155 <inputs>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	156 <conditional name="options_usage">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	157 <param name="rad_analysis_type" type="select" label="Select your usage">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	158 <option value="genetic" selected="true">Genetic map</option>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	159 <option value="population">Population</option>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	160 </param>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	161 <when value="genetic">
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	162 <param name="parent_sequences" argument="-p" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing parent sequences" help="Files containing parent sequences from a mapping cross (only R1 reads). Dataset names will be used as sample name (no space allowed)." />
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	163
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	164 <param name="progeny_sequences" argument="-r" format="fastqsanger,fasta" type="data" multiple="true" optional="true" label="Files containing progeny sequences" help="files containing progeny sequences from a mapping cross (only R1 reads). Dataset names will be used as sample name (no space allowed)." />
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	165
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	166 <param name="cross_type" argument="-A" type="select" label="Cross type">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	167 <expand macro="cross_types"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	168 </param>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	169 </when>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	170 <when value="population">
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	171 <param name="individual_sample" argument="-s" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing an individual sample from a population" help="files containing an individual sample from a population (only R1 reads). Dataset names will be used as sample name (no space allowed)." />
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	172 <param name="popmap" argument="-O" type="data" format="tabular,txt" label="Specify a population map" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	173 </when>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	174 </conditional>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	175
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	176 <!-- stack assembly options -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	177 <section name="assembly_options" title="Assembly options" expanded="false">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	178 <param name="m" argument="-m" type="integer" value="" optional="true" label="Minimum number of identical raw reads required to create a stack" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	179 <param name="P" argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	180 <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	181 <param name="N" argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" />
4 998dfec32bde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f iuc parents: 3 diff changeset	182 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog"/>
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	183
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	184 <param name="t" argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	185 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	186 </section>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	187
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	188 <!-- SNP Model options -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	189 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	190 <expand macro="snp_options"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	191 </section>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	192 </inputs>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	193 <outputs>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	194 <data format="txt" name="output_log" label="denovo_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/denovo_map.log" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	195
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	196 <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	197 <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	198 <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	199
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	200 <expand macro="genotypes_output_light"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	201 <expand macro="populations_output_light"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	202
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	203 <collection name="tags" type="list" label="Assembled loci from ${on_string}">
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	204 <discover_datasets pattern="(?P<name>.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	205 </collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	206
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	207 <collection name="snps" type="list" label="Model calls from each locus on ${on_string}">
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	208 <discover_datasets pattern="(?P<name>.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	209 </collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	210
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	211 <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus on ${on_string}">
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	212 <discover_datasets pattern="(?P<name>.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	213 </collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	214
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	215 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	216 <discover_datasets pattern="(?P<name>.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	217 </collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	218
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	219 <collection name="all_output" type="list" label="Full output from denovo_map on ${on_string}">
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	220 <discover_datasets pattern="(?P<name>.+\.(tags\|snps\|alleles\|matches))\.tsv$" ext="tabular" directory="stacks_outputs" />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	221 <discover_datasets pattern="(?P<name>.+\.(haplotypes\|genotypes\|markers\|hapstats\|sumstats\|sumstats_summary))\.tsv$" ext="tabular" directory="stacks_outputs" />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	222 <discover_datasets pattern="(?P<name>.+\.(genotypes))\.(loc\|txt)$" ext="txt" directory="stacks_outputs" />
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	223 </collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	224 </outputs>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	225
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	226 <tests>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	227 <test>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	228 <param name="options_usage\|rad_analysis_type" value="genetic"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	229 <param name="options_usage\|parent_sequences" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	230 <output name="output_log">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	231 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	232 <has_text text="denovo_map.pl completed" />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	233 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	234 </output>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	235
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	236 <!-- catalog -->
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	237 <output name="catalogtags">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	238 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	239 <has_text text="catalog generated on" />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	240 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	241 </output>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	242 <output name="catalogsnps">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	243 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	244 <has_text text="catalog generated on" />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	245 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	246 </output>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	247 <output name="catalogalleles">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	248 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	249 <has_text text="catalog generated on" />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	250 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	251 </output>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	252
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	253 <!-- genotypes -->
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	254 <output name="out_generic_haplo">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	255 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	256 <has_text text="Catalog ID" />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	257 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	258 </output>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	259 <output name="out_sql_markers">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	260 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	261 <has_text text="Total Genotypes" />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	262 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	263 </output>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	264 <output name="out_joinmap">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	265 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	266 <has_text text="batch_1.genotypes_" />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	267 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	268 </output>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	269 <output name="out_sql_genotypes">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	270 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	271 <has_text text="SQL ID" />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	272 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	273 </output>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	274
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	275 <!-- samples -->
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	276 <output_collection name="tags">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	277 <element name="PopA_01.tags">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	278 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	279 <has_text text="generated on " />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	280 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	281 </element>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	282 </output_collection>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	283 <output_collection name="snps">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	284 <element name="PopA_01.snps">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	285 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	286 <has_text text="generated on " />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	287 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	288 </element>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	289 </output_collection>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	290 <output_collection name="alleles">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	291 <element name="PopA_01.alleles">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	292 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	293 <has_text text="generated on " />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	294 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	295 </element>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	296 </output_collection>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	297 <output_collection name="matches">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	298 <element name="PopA_01.matches">
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	299 <assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	300 <has_text text="generated on " />
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	301 </assert_contents>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	302 </element>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	303 </output_collection>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	304 </test>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	305
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	306 <test>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	307 <param name="options_usage\|rad_analysis_type" value="genetic"/>
bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	308 <param name="options_usage\|parent_sequences" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	309 <param name="options_usage\|progeny_sequences" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	310 <output name="output_log">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	311 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	312 <has_text text="denovo_map.pl completed" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	313 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	314 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	315
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	316 <!-- catalog -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	317 <output name="catalogtags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	318 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	319 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	320 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	321 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	322 <output name="catalogsnps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	323 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	324 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	325 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	326 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	327 <output name="catalogalleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	328 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	329 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	330 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	331 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	332
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	333 <!-- genotypes -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	334 <output name="out_generic_haplo">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	335 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	336 <has_text text="Catalog ID" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	337 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	338 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	339 <output name="out_sql_markers">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	340 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	341 <has_text text="Total Genotypes" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	342 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	343 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	344 <output name="out_joinmap">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	345 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	346 <has_text text="batch_1.genotypes_" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	347 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	348 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	349 <output name="out_sql_genotypes">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	350 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	351 <has_text text="SQL ID" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	352 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	353 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	354
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	355 <!-- samples -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	356 <output_collection name="tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	357 <element name="PopA_01.tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	358 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	359 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	360 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	361 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	362 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	363 <output_collection name="snps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	364 <element name="PopA_01.snps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	365 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	366 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	367 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	368 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	369 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	370 <output_collection name="alleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	371 <element name="PopA_01.alleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	372 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	373 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	374 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	375 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	376 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	377 <output_collection name="matches">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	378 <element name="PopA_01.matches">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	379 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	380 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	381 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	382 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	383 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	384 </test>
3 bab631cc9f64 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393 iuc parents: 0 diff changeset	385
0 9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	386 <test>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	387 <param name="options_usage\|rad_analysis_type" value="population"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	388 <param name="options_usage\|individual_sample" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq,demultiplexed/PopA_03.1.fq,demultiplexed/PopA_04.1.fq,demultiplexed/PopB_01.1.fq,demultiplexed/PopB_02.1.fq,demultiplexed/PopB_03.1.fq,demultiplexed/PopB_04.1.fq" ftype="fastqsanger" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	389 <param name="options_usage\|popmap" value="denovo_map/popmap.tsv" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	390 <output name="output_log">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	391 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	392 <has_text text="denovo_map.pl completed" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	393 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	394 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	395
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	396 <!-- catalog -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	397 <output name="catalogtags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	398 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	399 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	400 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	401 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	402 <output name="catalogsnps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	403 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	404 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	405 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	406 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	407 <output name="catalogalleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	408 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	409 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	410 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	411 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	412
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	413 <!-- populations -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	414 <output name="out_haplotypes">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	415 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	416 <has_text text="PopA_01" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	417 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	418 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	419 <output name="out_hapstats">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	420 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	421 <has_text text="Smoothed Gene Diversity" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	422 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	423 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	424 <output name="out_populations_log">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	425 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	426 <has_text text="populations version" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	427 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	428 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	429 <output name="out_sumstats_sum">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	430 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	431 <has_text text="Polymorphic Sites" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	432 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	433 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	434 <output name="out_sumstats">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	435 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	436 <has_text text="Smoothed Pi" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	437 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	438 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	439
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	440 <!-- samples -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	441 <output_collection name="tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	442 <element name="PopA_01.tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	443 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	444 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	445 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	446 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	447 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	448 <output_collection name="snps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	449 <element name="PopA_01.snps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	450 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	451 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	452 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	453 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	454 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	455 <output_collection name="alleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	456 <element name="PopA_01.alleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	457 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	458 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	459 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	460 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	461 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	462 <output_collection name="matches">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	463 <element name="PopA_01.matches">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	464 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	465 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	466 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	467 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	468 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	469 </test>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	470 </tests>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	471
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	472 <help>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	473 <![CDATA[
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	474 .. class:: infomark
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	475
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	476 What it does
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	477
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	478 This program will run each of the Stacks components: first, running ustacks on each of the samples specified, building loci and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci that were marked as 'parents' or 'samples' on the command line, and finally, sstacks will be executed to match each sample against the catalog. A bit more detail on this process can be found in the FAQ. The denovo_map.pl program will also load the results of each stage of the analysis: individual loci, the catalog, and matches against the catalog into the database (although this can be disabled). After matching, the program will build a database index to speed up access (index_radtags.pl) and enable web-based filtering.
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	479
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	480 --------
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	481
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	482 Input files
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	483
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	484 FASTQ, FASTA
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	485
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	486 - Population map::
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	487
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	488 indv_01 1
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	489 indv_02 1
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	490 indv_03 1
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	491 indv_04 2
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	492 indv_05 2
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	493 indv_06 2
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	494
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	495
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	496 Output files
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	497
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	498
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	499 - XXX.tags.tsv file:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	500
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	501 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	502
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	503 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	504
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	505
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	506 - XXX.snps.tsv file:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	507
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	508 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	509
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	510 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	511
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	512
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	513 - XXX.alleles.tsv file:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	514
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	515 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	516
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	517
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	518 - XXX.matches.tsv file:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	519
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	520 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	521
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	522 Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample.
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	523
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	524
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	525 - other files:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	526
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	527 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	528
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	529 @STACKS_INFOS@
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	530 ]]>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	531 </help>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	532 <expand macro="citation" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty iuc parents: diff changeset	533 </tool>

Mercurial > repos > iuc > stacks_denovomap

annotate stacks_denovomap.xml @ 4:998dfec32bde draft