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view pscan_chip/pscan_chip.xml @ 7:06e6fa9771e2 draft

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author fz77
date Wed, 12 Nov 2014 10:29:28 -0500
parents dc406e234eca
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<tool id="pscan_chip" name="PscanChIP" version="1.0.0">
  <description>PscanChIP</description>
  <requirements>
  	<requirement type="binary">twoBitToFa</requirement>
  	<requirement type="binary">pscan_chip_g</requirement>
  </requirements>
	
  <!--command>
  read_distrib $input_map_file $input_pos_file $region_size $bin_size $shift_size '$output_freq' '$output_freq_all'
  </command-->
  <command>
  #if $profile_type.profiles == "/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/jaspar_vertebrates.wil"
  	#if $profile_type.BG_Jaspar.value == "none"
  		#if $selected.value == ""
  			pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet
  		#else
  			pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -m $selected
  		#end if
  	#else
  		#if $selected.value == ""
  			pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -bg /home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/BG/$profile_type.BG_Jaspar
  		#else
  			pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -bg /home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/BG/$profile_type.BG_Jaspar -m $selected
  		#end if
  	#end if
  #else if $profile_type.profiles == "/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/transfac_vertebrates.wil"
  	#if $profile_type.BG_Transfac.value == "none"
  		#if $selected.value == ""
  			pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet
  		#else
  			pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -m '$selected'
  		#end if
  	#else
  		#if $selected.value == ""
  			pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -bg /home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/BG/$profile_type.BG_Transfac
  		#else
  			pscan_chip_g -r $input_bed_file -M $profile_type.profiles -g $genomeSource -go $main_output -2bit -quiet -bg /home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/BG/$profile_type.BG_Transfac -m '$selected'
  		#end if
  	#end if
  #else
  	#if $selected.value == ""
  		pscan_chip_g -r $input_bed_file -M $profile_type.custom_matrix_file -g $genomeSource -go $main_output -2bit -quiet
  	#else
  		pscan_chip_g -r $input_bed_file -M $profile_type.custom_matrix_file -g $genomeSource -go $main_output -2bit -quiet -m $selected
  	#end if
  #end if
  </command>


  <inputs>
    <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Peaks File" />
    <param name="genomeSource" type="select" label="Use a built in reference genome.">
   	<options from_data_table="2bit_genomes">
    		<validator type="no_options" message="No genomes are available for the selected input dataset"/>
    	</options>
    </param>
    <conditional name="profile_type">
    	<param name="profiles" type="select" label="Select binding profiles descriptors">
    		<option value="/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/jaspar_vertebrates.wil" selected="true">Jaspar (vertebrates)</option>
    		<option value="/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/transfac_vertebrates.wil">Transfac (vertebrates)</option>
    		<option value="data">From file</option>
    	</param>

    	<when value="/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/jaspar_vertebrates.wil">
    		<param name="BG_Jaspar" type="select" label="Select background">
    			<options from_data_table="jaspar_pchip_bg">
    			</options>
    		</param>
    	</when>

	<when value="/home/galaxy/galaxy-dist/tools/ngs_beacon/pscan_chip/transfac_vertebrates.wil">
		<param name="BG_Transfac" type="select" label="Select Background">
	        	<options from_data_table="transfac_pchip_bg">
	                </options>
	        </param>
	</when>

	<when value="data">
		<param name="custom_matrix_file" type="data" label="Select dataset"/>
	</when>
    </conditional>
    <param name="selected" type="text" size="16" value="" label="Matrix ID (leave blank to perform standard run)" >
    <sanitizer sanitize="false"/>
    </param>
  </inputs>
  <outputs>
    <data name="main_output" metadata_source="input_bed_file" format="tabular" label="${tool.name} on ${on_string} results"/>
  </outputs>


  <help>
  PscanChIP Galaxy plug-in. Visit Pscan-ChIP home page at http://www.beaconlab.it/pscan_chip_dev to learn more on Pscan-ChIP.
  </help>
</tool>