view hmcan_wrapper.xml @ 2:39100c5526b3 draft default tip

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<tool id="hmcan" name="HMCan" version="1.11">
	<description>Histone Modification detection in Cancer samples</description>
	<requirements>
    	<container type="docker">institutcuriengsintegration/hmcan:1.0</container>
	</requirements>
	<command interpreter="python">hmcan_wrapper.py '${input_chip_file}' '${input_control_file}' '${hmcan_config_file}' '${gccount_config_file}' '${project_name}' '${output_peaks_file}' '${output_regions_file}' '${output_density_file}' '${output_posterior_proba_file}' '${hmcan_log_report}' '$genome['chr_len_file']' '${file_format}' '${genome.genome_selector}' '${__root_dir__}' 2> '${hmcan_log_report}'</command>


<!-- 
###NoteToSelf:
in this version, you still need to :
-Get the correct paths to mappability.GEM
- go to hmcan_wrapper.py
- set the correct paths to binary files (HMCAN, GCCOUNT)
-->   

	<!-- INPUT DESCRIPTION -->
	<inputs> 
		<!-- project name-->
		<param name="project_name" type="text" size="20" label="Project name" help="NOTE: spaces are not allowed.">
			<validator type="empty_field" message="You must specify a file name."/>
		</param>
		
		<!-- input files NB: format= only if attribute type is data, formats (bed,sam..) are contained in datatypes_conf.xml.sample f-->
		<param name="input_chip_file" type="data" format="bed,sam,bam" label="ChIP seq alignment file"/>
		<param name="input_control_file" type="data" format="bed,sam,bam" label="Control alignment file"/>		
		<!-- format-->
		<param name="file_format" type="select" label="Select alignment format">
			<option value="bed" selected="true">BED</option>
			<option value="bam">BAM</option>
			<option value="sam">SAM</option>	
		</param>
		<!-- lengths-->		
		<param name="min_len" type="integer" value="145" label="Minumum fragment length used in the ChIP-seq experiment"/>
		<param name="med_len" type="integer" value="150" label="Median fragment length used in the ChIP-seq experiment"/>
		<param name="max_len" type="integer" value="155" label="Maximum fragment length used in the ChIP-seq experiment"/>
		<param name="bin_size" type="integer" value="50" label="Bin size"/>
		<param name="merge_dist" type="integer" value="2000" label="Merge distance" help=" Maximum distance to merge single peaks into a region.This parameter should be set with respect to the nature of the mark; narrow marks (e.g H3K4me1, H3K4me3) can cover 200bp-2Kb, wide marks (e.g. H3K36me3, H3K27me3) can cover 10Kb-100Kb."/>
		
		<param name="p_value" type="float" value="0.01" label="P Value"/>
		<param name="input_blacklist_file" type="data" format="bed" label=".BED file with blacklist regions" help="An example of such a bed file for hg19 can be found here: http://xfer.curie.fr/get/GaQHuEopJTw/hg19-blacklist.bed"/>
		<!-- SELECT GENOME UNDER STUDY (hg19, hg18, hg38,mm9, mm10)-->
		<!-- Each genome is associated with :
		  ** Mappability Track 
		  ** chr_length file: -->
		<conditional name="genome">
			<param name="genome_selector" type="select" label="Select the version of the genome under study">
				<option value="hg19" selected="true">hg19</option>
				<option value="hg18">hg18</option>
				<option value="mm10">mm10</option>	
				<option value="mm9">mm9</option>
			</param>
			<!-- set the correct genome_path / mappability / chr_len for all genomes! -->
			<when value="hg18">
				<param name="genome_path" type="hidden" value="/galaxy/annotations"/>
				<param name="mappability" type="hidden" value="/galaxy/annotations"/> 
				<param name="chr_len_file" type="hidden" value="/galaxy/annotations"/>
			</when>	
			<when value="hg19">
				<param name="genome_path" type="hidden" value="/galaxy/annotations"/>
				<param name="mappability" type="hidden" value="/galaxy/annotations"/> 
				<param name="chr_len_file" type="hidden" value="/galaxy/annotations"/>
			</when>	
			<when value="mm9">
				<param name="genome_path" type="hidden" value="/galaxy/annotations"/>
				<param name="mappability" type="hidden" value="/galaxy/annotations"/> 
				<param name="chr_len_file" type="hidden" value="/galaxy/annotations"/>
			</when>
			<when value="mm10">
				<param name="genome_path" type="hidden" value="/galaxy/annotations"/>
				<param name="mappability" type="hidden" value="/galaxy/annotations"/> 
				<param name="chr_len_file" type="hidden" value="/galaxy/annotations"/>
			</when>
			
		</conditional>
		<!-- Booleans  + LOGING-->
		<param name="print_wig" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Print density profil in WIG file" />
		<param name="print_posterior_proba" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Print bins posterior probabilites in WIG format" />
		<param name="print_logging" type="boolean" truevalue= "True" falsevalue="False" checked="true" label="Print HMCan log"/>
		<!-- HMM advanced-->
		<conditional name="option_type">
			<param name="option_type_selector" type="select" label="Advanced options">
				<option value="basic" selected="true">Hide advanced options</option>
				<option value="advanced">Show advanced options</option>
			</param>
			<!-- WHENS-->
			<when value="basic"/>
			<when value="advanced"> <!-- if advanced create HHM parameters form-->
				<param name="max_iter" type="integer" value="20" label="Maximun interation for HMCan algorithm"/>
				<param name="iteration_score_threshold" type="integer" value="2" label="Iteration score threshold" help="minimum score to accept a peak into the next iteration"/>
				<param name="final_score_threshold" type="integer" value="0" label="Score threshold" help="score threshold to report peak or regions"/>
			</when>
			
		</conditional>
	</inputs>
	
	<!-- OUTPUT DESCRIPTION -->
	<outputs>
		<data name="output_peaks_file" format="bed" label="${project_name} histone peaks (bed)"/> 
		<data name="output_regions_file" format="bed" label="${project_name} histone regions (bed)"/>
		
		<!-- <filter>if this is true, data will be created as normal</filter> -->
		<data name="output_density_file" format="wig" label="${project_name} density profile (wig)">
			<filter>print_wig==True</filter>
		</data>
		
		<data name="output_posterior_proba_file" format="wig" label="${project_name} peaks prosterior probability (wig)">
			<filter>print_posterior_proba==True</filter>
		</data>
		
		<data name="hmcan_log_report" format="txt" label="${tool.name} log report (txt)">
			<filter> print_logging==True</filter>
		</data>
	</outputs>

	<configfiles>
		<configfile name="hmcan_config_file">format ${file_format}
GCIndex  
genomePath $genome['genome_path']  <!--  /data/tmp/amira/example_seq-->     
minLength ${min_len}
medLength ${med_len}
maxLength ${max_len}
smallBinLength ${bin_size}
largeBinLength 
pvalueThreshold ${p_value}
mergeDistance ${merge_dist}
blackListFile ${input_blacklist_file}
#if str($option_type ['option_type_selector'])=="advanced":
iterationThreshold ${option_type['iteration_score_threshold']} 	
finalThreshold ${option_type['final_score_threshold']}
maxIter ${option_type['max_iter']} 
#else:
iterationThreshold 5
finalThreshold 10
maxIter 20		
#end if		
PrintWig ${print_wig} 
PrintPosterior ${print_posterior_proba}
		</configfile>
		<configfile name="gccount_config_file">[general]
		
window =  
step = 
outputDir = . 
chrFiles = $genome['genome_path']
chrLenFile = $genome['chr_len_file']
gemMappabilityFile = $genome['mappability']
		</configfile>
	</configfiles>
  
	<help>
**What it does**

HMCan detects histone modifications in cancer samples.

**Cite HMCan**

If you use this tool, please cite : HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.Haitham Ashoor; Aurelie Herault; Aurelie Kamoun; Francois Radvanyi; Vladimir B. Bajic; Emmanuel Barillot; Valentina Boeva.Bioinformatics 2013; doi: 10.1093/bioinformatics/btt524
   
	</help>
</tool>