macs21: macs21_wrapper.xml annotate

annotate macs21_wrapper.xml @ 8:78c15c0a96ae draft

Uploaded new version with minor fixes and updates to help text.

author	pjbriggs
date	Tue, 21 Apr 2015 10:33:52 -0400
parents	344dd37d1704
children	7aecd0908b3c

rev	line source
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	1 <tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-2">
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	2 <requirements>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	3 <requirement type="package" version="2.7">python</requirement>
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	4 <requirement type="package" version="1.9">numpy</requirement>
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	5 <requirement type="package" version="2.1.0.20140616">macs2</requirement>
6 344dd37d1704 Add dependency on R. pjbriggs parents: 5 diff changeset	6 <requirement type="package" version="3.1.2">R</requirement>
5 9f6d5cae9181 Uploaded yet another attempt to fix tool dependencies! pjbriggs parents: 4 diff changeset	7 <requirement type="package" version="1.0">ucsc_tools_for_macs21</requirement>
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	8 </requirements>
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	9 <description>Model-based Analysis of ChIP-Seq</description>
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	10 <command interpreter="python">
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	11 macs21_wrapper.py
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	12 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	13 ## Major command
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	14 $major_command.major_command_selector
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	15 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	16 ## ChIP-seq input
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	17 $major_command.input_chipseq_file1
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	18 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	19 ## ChIP-seq control
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	20 #if str($major_command.input_control_file1) != 'None'
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	21 -c $major_command.input_control_file1
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	22 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	23 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	24 ## Call peaks
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	25 #if str($major_command.major_command_selector) == 'callpeak'
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	26 --format=$major_command.input_chipseq_file1.extension
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	27 --name="$experiment_name"
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	28 --bw=$major_command.bw
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	29 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	30 ## Genome size
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	31 #if str($major_command.genome_size.gsize) == ''
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	32 --gsize=$major_command.genome_size.user_defined_gsize
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	33 #else:
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	34 --gsize=$major_command.genome_size.gsize
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	35 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	36 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	37 ## Broad peaks
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	38 #if str($major_command.broad_options.broad_regions) == 'broad'
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	39 --broad --broad-cutoff=$major_command.broad_options.broad_cutoff
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	40 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	41 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	42 ## (no)model options
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	43 #if str($major_command.nomodel_type.nomodel_type_selector) == 'nomodel'
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	44 --nomodel --extsize=$major_command.nomodel_type.extsize
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	45 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	46 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	47 ## pq value select options
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	48 #if str($major_command.pq_options.pq_options_selector) == 'qvalue'
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	49 --qvalue=$major_command.pq_options.qvalue
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	50 #else
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	51 --pvalue=$major_command.pq_options.pvalue
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	52 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	53 ##
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	54 ## Bedgraph options
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	55 #if $major_command.bdg_options.bdg == True
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	56 -B $major_command.bdg_options.spmr
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	57 #end if
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	58 ##
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	59 ## Advanced options
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	60 #if str($major_command.advanced_options.advanced_options_selector) == 'on'
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	61 --mfold $major_command.advanced_options.mfoldlo $major_command.advanced_options.mfoldhi
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	62 $major_command.advanced_options.nolambda
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	63 $major_command.advanced_options.call_summits
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	64 #if str($major_command.advanced_options.keep_duplicates.keep_dup) == ''
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	65 --keep-dup $major_command.advanced_options.keep_duplicates.maximum_tags
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	66 #else
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	67 --keep-dup $major_command.advanced_options.keep_duplicates.keep_dup
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	68 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	69 #else
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	70 ## Defaults if advanced options not set
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	71 --mfold 10 30 --keep-dup 1
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	72 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	73 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	74 ## Output files
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	75 --output-summits=$output_summits_bed_file
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	76 --output-extra-files=$output_extra_files
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	77 --output-extra-files-path=$output_extra_files.files_path
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	78 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	79 ## Narrow/broad peak outputs
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	80 #if str($major_command.broad_options.broad_regions) == 'broad'
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	81 --output-broadpeaks=$output_broadpeaks_file
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	82 --output-gappedpeaks=$output_gappedpeaks_file
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	83 #else
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	84 --output-narrowpeaks=$output_narrowpeaks_file
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	85 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	86 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	87 ## Bedgraph outputs
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	88 #if str($major_command.bdg_options.bdg) == 'True'
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	89 --output-pileup=$output_treat_pileup_file
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	90 --output-lambda-bedgraph=$output_lambda_bedgraph_file
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	91 #if str($major_command.bdg_options.make_bigwig) == 'True'
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	92 --output-bigwig=$output_bigwig_file
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	93 --length=$GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${major_command.input_chipseq_file1.dbkey}.len
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	94 #end if
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	95 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	96 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	97 ## XLS/interval output
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	98 #if str($major_command.xls_to_interval) == 'True'
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	99 --output-xls-to-interval=$output_xls_to_interval_peaks_file
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	100 #else
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	101 --output-peaks=$output_peaks_file
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	102 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	103 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	104 ##
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	105 ## Compare .bdg files
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	106 #if str($major_command.major_command_selector) == 'bdgcmp'
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	107 -m $major_command.bdgcmp_options.bdgcmp_options_selector
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	108 -p $major_command.pseudocount
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	109 --output-bdgcmp $output_bdgcmp_file
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	110 #end if
d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	111 </command>
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	112 <inputs>
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	113 <!--experiment name used as base for output file names -->
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	114 <param name="experiment_name" type="text" value="MACS2.1.0 in Galaxy" size="50"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	115 label="Experiment Name"/>
1 d0986d2be693 Substantial reimplementation of internals, also renamed id and version. pjbriggs parents: 0 diff changeset	116 <!--select a major MACS2 command-->
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	117 <conditional name="major_command">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	118 <param name="major_command_selector" type="select" label="Select action to be performed">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	119 <option value="callpeak">Peak Calling</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	120 <option value="bdgcmp">Compare .bdg Files</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	121 </param>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	122 <!--callpeak option of macs2-->
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	123 <when value="callpeak">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	124 <!--choose 'broad' or 'narrow' regions-->
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	125 <conditional name="broad_options">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	126 <param name="broad_regions" type="select" label="Type of region to call"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	127 help="Broad regions are formed by linking nearby enriched regions">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	128 <option value="" selected="true">Narrow regions</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	129 <option value="broad">Broad regions</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	130 </param>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	131 <when value="broad">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	132 <param name="broad_cutoff" type="float"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	133 label="Cutoff for broad regions"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	134 value="0.1" help="default: 0.1 (--broad-cutoff)"/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	135 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	136 </conditional>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	137 <param name="input_chipseq_file1" type="data" format="bed,sam,bam"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	138 label="ChIP-seq read file" />
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	139 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	140 label="ChIP-seq control read file" />
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	141 <conditional name="genome_size">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	142 <param name="gsize" type="select" label="Effective genome size"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	143 help="Either pre-defined (for common organisms), or user-defined (--gsize)">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	144 <option value="hs" selected="true">Human (2.7e9)</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	145 <option value="mm">Mouse (1.87e9)</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	146 <option value="ce">C. elegans (9e7)</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	147 <option value="dm">Fruitfly (1.2e8)</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	148 <option value="">User-defined</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	149 </param>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	150 <when value="">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	151 <!-- User-defined effective genome size -->
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	152 <param name="user_defined_gsize" type="float" value=""
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	153 label="Enter effective genome size (number of bases)"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	154 help="e.g. '1.0e+9' or '1000000000'" />
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	155 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	156 </conditional>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	157 <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	158 <param name="xls_to_interval" label="Include XLS file from MACS"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	159 type="boolean" truevalue="True" falsevalue="False" checked="True"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	160 help="MACS2 XLS file will be output to the history in 'interval' format (suitable for subsequent analysis in Galaxy). Note that start positions are 1-based."/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	161
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	162 <conditional name="bdg_options">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	163 <param name="bdg"
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	164 label="Save treatment and control lambda pileups in bedGraph"
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	165 type="boolean" truevalue="-B" falsevalue="" checked="False" />
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	166 <when value="-B">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	167 <param name="spmr"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	168 type="boolean" truevalue="--SPMR" falsevalue="" checked="False"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	169 label="Save signal per million reads for fragment pileup profiles"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	170 help="(--SPMR)" />
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	171 <param name="make_bigwig" type="boolean" checked="True"
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	172 truevalue="True" falsevalue=""
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	173 label="Also generate bigWig file from bedGraph"
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	174 help="bigWig file can used in subsequent analyses e.g. CEAS" />
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	175 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	176 <when value="">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	177 <!-- Display nothing -->
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	178 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	179 </conditional>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	180
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	181 <conditional name="pq_options">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	182 <param name="pq_options_selector" type="select"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	183 label="Select p-value or q-value" help="default uses q-value">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	184 <option value="qvalue">q-value</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	185 <option value="pvalue">p-value</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	186 </param>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	187 <when value="pvalue">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	188 <param name="pvalue" type="float"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	189 label="p-value cutoff for binding region detection"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	190 value="1e-2" help="default: 1e-2 (--pvalue)"/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	191 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	192 <when value="qvalue">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	193 <param name="qvalue" type="float"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	194 label="q-value cutoff for binding region detection"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	195 value="0.01" help="default: 0.01 (--qvalue)"/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	196 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	197 </conditional>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	198 <conditional name="advanced_options">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	199 <param name="advanced_options_selector" type="select"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	200 label="Display advanced options">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	201 <option value="off">Hide</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	202 <option value="on">Display</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	203 </param>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	204 <when value="on">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	205 <param name="mfoldlo" type="integer"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	206 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (lower-limit)"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	207 value="10" help="(--mfold)"/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	208 <param name="mfoldhi" type="integer"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	209 label="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (upper-limit)"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	210 value="30" help="(--mfold)"/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	211 <param name="nolambda"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	212 label="Use fixed background lambda as local lambda for every binding region"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	213 type="boolean" truevalue="--nolambda" falsevalue="" checked="False"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	214 help="(--nolambda)"/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	215 <param name="call_summits"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	216 label="Detect subpeaks within binding region"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	217 type="boolean" truevalue="--call-summits" falsevalue="" checked="False"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	218 help="(--call-summits)"/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	219 <conditional name="keep_duplicates">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	220 <param name="keep_dup" type="select"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	221 label="Use of duplicate reads">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	222 <option value="auto">Automatically calculate maximum number of duplicates to keep (auto)</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	223 <option value="all">Use all duplicates (all)</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	224 <option value="" selected="true">Manually specify maxium number of duplicates</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	225 </param>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	226 <when value="">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	227 <param name="maximum_tags" type="integer" value="1"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	228 label="Maxium number of duplicated tags to keep at each location"/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	229 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	230 </conditional>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	231 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	232 <when value="off">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	233 <!--display nothing-->
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	234 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	235 </conditional>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	236 <conditional name="nomodel_type">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	237 <param name="nomodel_type_selector" type="select" label="Build Model">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	238 <option value="nomodel">Do not build the shifting model (--nomodel enabled)</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	239 <option value="create_model" selected="true">Build the shifting model (--nomodel disabled)</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	240 </param>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	241 <when value="nomodel">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	242 <param name="extsize" type="integer" label="Arbitrary extension size in bp" value="200" help="Used as fragment size to extend each read towards 3' end (--extsize)"/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	243 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	244 </conditional>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	245 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	246
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	247 <!--callpeak option of macs2-->
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	248 <when value="bdgcmp">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	249 <param name="input_chipseq_file1" type="data" format="bed,sam,bam"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	250 label="ChIP-seq read file" />
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	251 <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	252 label="ChIP-seq control read file" />
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	253 <param name="pseudocount" type="float" label="Set pseudocount" value="0.00001"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	254 help="default: 0.00001 (-p)"/>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	255 <conditional name="bdgcmp_options">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	256 <param name="bdgcmp_options_selector" type="select"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	257 label="Select action to be performed">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	258 <option value="ppois">ppois</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	259 <option value="qpois">qpois</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	260 <option value="subtract">subtract</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	261 <option value="logFE">logFE</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	262 <option value="FE">FE</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	263 <option value="logLR">logLR</option>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	264 </param>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	265 </conditional>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	266 </when>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	267 </conditional>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	268 </inputs>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	269
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	270 <outputs>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	271 <!--callpeaks output-->
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	272 <data name="output_extra_files" format="html"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	273 label="${tool.name}: callpeak on ${on_string} (html report)">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	274 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	275 </data>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	276 <data name="output_summits_bed_file" format="bed"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	277 label="${tool.name}: callpeak on ${on_string} (summits: bed)">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	278 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	279 </data>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	280 <data name="output_peaks_file" format="xls"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	281 label="${tool.name}: callpeak on ${on_string} (peaks: xls)">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	282 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	283 <filter>major_command['xls_to_interval'] is False</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	284 </data>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	285 <data name="output_narrowpeaks_file" format="interval"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	286 label="${tool.name}: callpeak on ${on_string} (peaks: narrowPeak)">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	287 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	288 <filter>major_command['broad_options']['broad_regions'] == ''</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	289 </data>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	290 <data name="output_broadpeaks_file" format="interval"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	291 label="${tool.name}: callpeak on ${on_string} (peaks: broadPeak)">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	292 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	293 <filter>major_command['broad_options']['broad_regions'] == 'broad'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	294 </data>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	295 <data name="output_gappedpeaks_file" format="interval"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	296 label="${tool.name}: callpeak on ${on_string} (peaks: gappedPeak)">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	297 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	298 <filter>major_command['broad_options']['broad_regions'] == 'broad'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	299 </data>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	300 <data name="output_xls_to_interval_peaks_file" format="interval"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	301 label="${tool.name}: callpeak on ${on_string} (peaks: interval)">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	302 <filter>major_command['xls_to_interval'] is True</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	303 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	304 </data>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	305 <data name="output_treat_pileup_file" format="bedgraph"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	306 label="${tool.name}: callpeak on ${on_string} (treat pileup: bedGraph)">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	307 <filter>major_command['bdg_options']['bdg'] is True</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	308 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	309 </data>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	310 <data name="output_lambda_bedgraph_file" format="bedgraph"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	311 label="${tool.name}: callpeak on ${on_string} (control lambda: bedGraph)">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	312 <filter>major_command['bdg_options']['bdg'] is True</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	313 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	314 </data>
2 15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	315 <data name="output_bigwig_file" format="bigwig"
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	316 label="${tool.name}: callpeak on ${on_string} (treat pileup: bigWig)">
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	317 <filter>major_command['major_command_selector'] == 'callpeak'</filter>
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	318 <filter>major_command['bdg_options']['bdg'] is True</filter>
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	319 <filter>major_command['bdg_options']['make_bigwig'] is True</filter>
15889783e759 Fix bugs in tool operation and update dependencies. pjbriggs parents: 1 diff changeset	320 </data>
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	321 <!--bdgcmp output-->
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	322 <data name="output_bdgcmp_file" format="bdg"
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	323 label="${tool.name}: bdgcmp on ${on_string} (bdg)">
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	324 <filter>major_command['major_command_selector'] == 'bdgcmp'</filter>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	325 </data>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	326 </outputs>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	327 <tests>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	328 <!--none yet for macs2-->
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	329 </tests>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	330 <help>
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	331 What it does
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	332
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	333 MACS (Model-based Analysis of ChIP-seq) provides algorithms for transcript
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	334 factor binding sites. The program can be used either for ChIP-Seq data alone,
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	335 or with control sample datat to improve specificity.
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	336
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	337 View the MACS2 documentation at:
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	338 https://github.com/taoliu/MACS/blob/master/README.rst
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	339
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	340 ------
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	341
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	342 Usage
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	343
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	344 The tool interfaces with two main functions in MACS:
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	345
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	346 * callpeaks (the main function) calls peaks from alignment results
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	347 * bdgcmp deducts noise by comparing two signal tracks in bedGraph format.
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	348
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	349 ------
fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	350
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	351 Credits
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	352
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	353 This Galaxy tool was based on the MACS2 tool hosted in the Galaxy toolshed at
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	354
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	355 * http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	356
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	357 (specifically the 16:14f378e35191 revision of the tool) which is credited to Ziru
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	358 Zhou. This version is a reimplemented version developed within the Bioinformatics
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	359 Core Facility at the University of Manchester, which uses more up-to-date Galaxy
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	360 syntax and adds some extra features.
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	361
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	362 The tool runs Tao Liu's MACS2 software:
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	363
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	364 * https://github.com/taoliu/MACS
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	365
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	366 The reference for MACS is:
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	367
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	368 * Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C,
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	369 Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS).
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	370 Genome Biol. 2008;9(9):R137.
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	371
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	372 Please kindly acknowledge both this Galaxy tool and the MACS2 package if you
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	373 use it.
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	374 </help>
8 78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	375 <citations>
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	376 <!--
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	377 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	378 Can be either DOI or Bibtex
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	379 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	380 -->
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	381 <citation type="doi">10.1186/gb-2008-9-9-r137</citation>
78c15c0a96ae Uploaded new version with minor fixes and updates to help text. pjbriggs parents: 6 diff changeset	382 </citations>
0 fdad0c8c0957 Uploaded initial version to test toolshed. pjbriggs parents: diff changeset	383 </tool>

Mercurial > repos > pjbriggs > macs21

annotate macs21_wrapper.xml @ 8:78c15c0a96ae draft