Mercurial > repos > fz77 > pscan_chip_test

diff pscan_chip/pscan_chip.xml @ 0:dc406e234eca draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fz77
date Wed, 12 Nov 2014 05:32:37 -0500
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pscan_chip/pscan_chip.xml	Wed Nov 12 05:32:37 2014 -0500
@@ -0,0 +1,94 @@
+<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>