ceas: ceas_wrapper.xml annotate

annotate ceas_wrapper.xml @ 4:4e2883bb058d draft

Synchronise version with one on main toolshed (version of 30/06/2015)

author	pjbriggs
date	Wed, 10 Aug 2016 11:04:42 -0400
parents	82df5af2995f
children	c9c4792d0876

rev	line source
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	1 <tool id="ceas" name="CEAS" version="1.0.2-2">
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	2 <description>Annotate intervals and scores with genome features</description>
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	3 <requirements>
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	4 <requirement type="package" version="1.2.5">python_mysqldb</requirement>
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	5 <requirement type="package" version="0.7.1">bx_python</requirement>
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	6 <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	7 <requirement type="package" version="1.0">ucsc_fetchChromSizes</requirement>
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	8 <requirement type="package" version="3.1.2">R</requirement>
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	9 </requirements>
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	10 <version_command>ceas --version 2>&1 \| tail -1</version_command>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	11 <command interpreter="bash">ceas_wrapper.sh
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	12 $bed_file ${gdb_file.fields.path}
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	13 $log_output $pdf_report $xls_output
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	14 #if (str($wig_file) != 'None')
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	15 #if (str($wig_file.ext) == 'bigwig')
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	16 --bigwig $wig_file
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	17 --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	18 #else
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	19 --wig $wig_file
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	20 #end if
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	21 #end if
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	22 #if (str($extra_bed_file) != 'None')
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	23 --ebed $extra_bed_file
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	24 #end if
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	25 #if (str($span) and int(str($span)) > 0)
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	26 --span $span
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	27 #end if
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	28 --sizes $sizes_lower,$sizes_middle,$sizes_upper
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	29 --bisizes $bisizes_lower,$bisizes_upper
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	30 --pf-res $profiling_resolution
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	31 --rel-dist $relative_distance</command>
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	32 <inputs>
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	33 <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" />
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	34 <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	35 help="If not supplied then only perform ChIP region annotation and gene-centered annotation" />
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	36 <param name="extra_bed_file" type="data" format="bed" label="BED file with extra regions of interest (e.g. non-coding regions)" optional="true" />
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	37 <param name="gdb_file" type="select" label="Gene annotation table">
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	38 <options from_data_table="ceas_annotations">
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	39 </options>
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	40 <filter name="dbkey" type="data_meta" ref="bed_file" key="dbkey" column="1" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	41 <validator type="no_options" message="No tables are available for the selected input"/>
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	42 </param>
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	43 <param name="span" type="integer"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	44 label="Span from TSS and TTS in the gene-centered annotation (bp)"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	45 help="ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates of promoter and downstream by ChIP regions (--span)" value="3000" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	46 <param name="sizes_lower" type="integer"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	47 label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	48 value="1000" help=" (--sizes)" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	49 <param name="sizes_middle" type="integer"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	50 label="Middle interval for promoter/downstream sizes (bp)" value="2000"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	51 help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	52 <param name="sizes_upper" type="integer"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	53 label="Upper interval for promoter/downstream sizes (bp)" value="3000"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	54 help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	55 <param name="bisizes_lower" type="integer"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	56 label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	57 help="(--bisizes)" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	58 <param name="bisizes_upper" type="integer"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	59 label="Upper interval for bidirectional-promoter sizes (bp)" value="5000"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	60 help="Values > 20000bp are automatically fixed to 20000bp (--bisizes)" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	61 <param name="profiling_resolution" type="integer"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	62 label="Wig profiling resolution (bp)" value="50"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	63 help="Warning: a number smaller than the wig interval (resolution) may cause aliasing error (--pf-res)" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	64 <param name="relative_distance" type="integer"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	65 label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	66 help="(--rel-dist)" />
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	67 </inputs>
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	68 <outputs>
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	69 <data name="log_output" format="txt" label="CEAS on ${on_string} (log output)" />
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	70 <data name="pdf_report" format="pdf" label="CEAS on ${on_string} (PDF report)" />
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	71 <data name="xls_output" format="interval" label="CEAS on ${on_string} (XLS output)" />
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	72 </outputs>
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	73 <tests>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	74 <test>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	75 <!-- Test with bed input only -->
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	76 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	77 <param name="gdb_file" value="galGal3_test" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	78 <output name="log_output" file="ceas_out1.log.re_match" compare="re_match"/>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	79 <output name="pdf_report" file="ceas_out1.pdf" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	80 <output name="xls_output" file="ceas_out1.xls" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	81 </test>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	82 <test>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	83 <!-- Test with bed & very small wig input -->
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	84 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	85 <param name="wig_file" value="ceas_in.wig" ftype="wig" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	86 <param name="gdb_file" value="galGal3_test" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	87 <output name="log_output" file="ceas_out2.log.re_match" compare="re_match"/>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	88 <output name="pdf_report" file="ceas_out2.pdf" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	89 <output name="xls_output" file="ceas_out2.xls" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	90 </test>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	91 <test>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	92 <!-- Test with bed & bigwig input -->
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	93 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	94 <param name="wig_file" value="ceas_in.bigwig" ftype="bigwig" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	95 <param name="gdb_file" value="galGal3_test" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	96 <output name="log_output" file="ceas_out3.log.re_match" compare="re_match"/>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	97 <output name="pdf_report" file="ceas_out3.pdf" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	98 <output name="xls_output" file="ceas_out3.xls" />
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	99 </test>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	100 </tests>
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	101 <help>
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	102 What it does
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	103
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	104 CEAS (Cis-regulatory Element Annotation System) is a tool for characterizing genome-wide
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	105 protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	106 binding factors. It provides statistics on ChIP enrichment at important genome features
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	107 such as specific chromosome, promoters, gene bodies, or exons, and infers genes most
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	108 likely to be regulated by a binding factor.
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	109
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	110 CEAS also enables biologists to visualize the average ChIP enrichment signals over
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	111 specific genomic features, allowing continuous and broad ChIP enrichment to be perceived
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	112 which might be too subtle to detect from ChIP peaks alone.
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	113
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	114 Usage
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	115
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	116 CEAS takes the following inputs:
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	117
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	118 * BED file with discrete ChIP regions (for example, the 'summits' output from the MACS
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	119 peak caller)
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	120 * WIG or bigWIG file with a continuous ChIP enrichment signal
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	121 * Gene annotation table (provided as reference data)
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	122
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	123 Optionally it can also take a BED file describing extra regions of interest (for example
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	124 non-coding regions).
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	125
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	126 The analysis modules are:
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	127
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	128 * ChIP region annotation: estimates the relative enrichment level of ChIP regions in
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	129 each gene feature with respect to the whole genome.
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	130 * Gene-centered annotation: identifies genes associated with ChIP regions to infer
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	131 the direct regulatory gene targets of the binding factor of interest.
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	132 * Average signal profiling within/near important genomic features: displays continuous
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	133 ChIP enrichment signal within/around important gene features to help visualize the
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	134 average binding patterns.
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	135
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	136 Background
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	137
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	138 This tool is compatible with the ceasBW version of CEAS from the Cistrome package
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	139 obtained from
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	140
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	141 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	142
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	143 (commit id d8c0751, datestamp 20140929). The CEAS code is under the
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	144 published-packages/CEAS/ subdirectory.
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	145
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	146 Cistrome data files and documentation can be found at
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	147
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	148 http://liulab.dfci.harvard.edu/CEAS/index.html
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	149
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	150 The CEAS user manual is available at http://liulab.dfci.harvard.edu/CEAS/usermanual.html
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	151 </help>
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	152 <citations>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	153 <!--
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	154 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	155 Can be either DOI or Bibtex
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	156 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	157 -->
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	158 <citation type="doi">10.1093/bioinformatics/btp479</citation>
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	159 </citations>
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	160 </tool>

Mercurial > repos > pjbriggs > ceas

annotate ceas_wrapper.xml @ 4:4e2883bb058d draft