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diff hifive.xml @ 0:0a9c76d80e33 draft

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planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
author sauria
date Fri, 05 Jun 2015 14:09:00 -0400
parents
children cb4f92e6fd4e
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hifive.xml	Fri Jun 05 14:09:00 2015 -0400
@@ -0,0 +1,390 @@
+<?xml version="1.0"?>
+<tool id="hifive" name="hifive" version="@WRAPPER_VERSION@.0">
+	<description>manipulate, analyze, and plot HiC and 5C chromatin interaction data</description>
+	<macros>
+		<import>hifive_macros.xml</import>
+	</macros>
+	<expand macro="requirements"/>
+	<expand macro="stdio"/>
+	<command><![CDATA[
+hifive
+
+$command.command_select
+
+#if str( $command.command_select ) == "hic-complete":
+	@HIC_NORMALIZE@
+	@HIC_FEND@
+	@HIC_SEQUENCE@
+	@HIC_CHROMOSOMES@
+	@HIC_PROJECT@
+	@HIC_RANGE@
+	-o $hic_comp_fends $hic_comp_data $hic_comp_project
+#end if
+#if str( $command.command_select ) == "fends":
+	@HIC_FEND@
+	$hic_fend_output
+#end if
+#if str( $command.command_select ) == "hic-data":
+	@HIC_SEQUENCE@
+	$fends $hic_data_output
+#end if
+#if str( $command.command_select ) == "hic-project":
+	@HIC_CHROMOSOMES@
+	@HIC_PROJECT@
+	@HIC_RANGE@
+	$hic_data $hic_project_output
+#end if
+#if str( $command.command_select ) == "hic-normalize":
+	@HIC_NORMALIZE@
+	@HIC_CHROMOSOMES@
+	@HIC_RANGE@
+	-o $hic_norm_output
+	$hic_project
+#end if
+#if str( $command.command_select ) == "hic-heatmap":
+	@HIC_CHROMOSOMES@
+	$command.trans1
+	@BINSIZE@
+	@HIC_DATATYPE@
+	@HIC_DYNAMIC@
+    #if str( $command.image.generate ) == "yes":
+		@IMAGE@
+		-i $hic_hm_image
+	#end if
+	$hic_project $hic_hm_output
+#end if
+#if str( $command.command_select ) == "hic-interval":
+	-c $command.chrom
+	#if $command.start:
+        -s $command.start
+    #end if
+    #if $command.stop:
+        -e $command.stop
+    #end if
+    #if $command.maxdist:
+        -m $command.maxdist
+    #end if
+	@BINSIZE@
+	@HIC_DATATYPE@
+	@HIC_DYNAMIC@
+    #if str( $command.image.generate ) == "yes":
+		@IMAGE@
+		@ROTATE@
+		-i $hic_int_image
+	#end if
+	$hic_project $hic_int_output
+#end if
+#if str( $command.command_select ) == "5c-complete":
+	@5C_NORMALIZE@
+	@5C_SEQUENCE@
+	@5C_REGIONS@
+	@5C_PROJECT@
+	@5C_RANGE@
+	-o $fivec_comp_frags $fivec_comp_data $fivec_comp_project
+	@5C_FRAGMENT@
+#end if
+#if str( $command.command_select ) == "fragments":
+	@5C_FRAGMENT@
+	$fivec_frag_output
+#end if
+#if str( $command.command_select ) == "5c-data":
+	@5C_SEQUENCE@
+	$fragments $fivec_data_output
+#end if
+#if str( $command.command_select ) == "5c-project":
+	@5C_REGIONS@
+	@5C_PROJECT@
+	@5C_RANGE@
+	$fivec_data $fivec_project_output
+#end if
+#if str( $command.command_select ) == "5c-normalize":
+	@5C_NORMALIZE@
+	@5C_REGIONS@
+	@5C_RANGE@
+	-o $fivec_norm_output
+	$fivec_project
+#end if
+#if str( $command.command_select ) == "5c-heatmap":
+	@5C_REGIONS@
+	$command.trans2
+	@BINSIZE@
+	@5C_DATATYPE@
+	@5C_DYNAMIC@
+    #if str( $command.image.generate ) == "yes":
+		@IMAGE@
+		-i $fivec_hm_image
+	#end if
+	$fivec_project $fivec_hm_output
+#end if
+#if str( $command.command_select ) == "5c-interval":
+	-c $command.region 
+	#if $command.start:
+        -s $command.start
+    #end if
+    #if $command.stop:
+        -e $command.stop
+    #end if
+	@BINSIZE@
+	@5C_DATATYPE@
+	@5C_DYNAMIC@
+    #if str( $command.image.generate ) == "yes":
+		@IMAGE@
+		@ROTATE@
+		-i $fivec_int_image
+	#end if
+	$fivec_project $fivec_int_output
+#end if
+ -q
+
+		]]></command>
+	<inputs>
+		<conditional name="command">
+			<param name="command_select" type="select" label="Select action to perform">
+				<option value="hic-complete">Complete HiC analysis</option>
+				<option value="5c-complete">Complete 5C analysis</option>
+				<option value="fends">Create HiC fend set</option>
+				<option value="hic-data">Create HiC data set</option>
+				<option value="hic-project">Create HiC project</option>
+				<option value="hic-normalize">Normalize HiC project</option>
+				<option value="hic-heatmap">Create HiC heatmap set</option>
+				<option value="hic-interval">Extract HiC interval</option>
+				<option value="fragments">Create 5C fragment set</option>
+				<option value="5c-data">Create 5C data set</option>
+				<option value="5c-project">Create 5C project</option>
+				<option value="5c-normalize">Normalize 5C project</option>
+				<option value="5c-heatmap">Create 5C heatmap set</option>
+				<option value="5c-interval">Extract 5C interval</option>
+			</param>
+			<when value="hic-complete">
+				<expand macro="hic_fend_xml"/>
+				<expand macro="hic_sequence_xml"/>
+				<expand macro="hic_chromosomes_xml"/>
+				<expand macro="hic_project_xml"/>
+				<expand macro="hic_range_xml"/>
+				<expand macro="hic_normalize_xml"/>
+			</when>
+			<when value="fends">
+				<expand macro="hic_fend_xml"/>
+			</when>
+			<when value="hic-data">
+		        <param format="h5" name="fends" type="data" label="HiFive fend file" optional="False"/>
+				<expand macro="hic_sequence_xml"/>
+			</when>
+			<when value="hic-project">
+		        <param format="h5" name="hic_data" type="data" label="HiFive HiC data file" optional="False"/>
+				<expand macro="hic_chromosomes_xml"/>
+				<expand macro="hic_project_xml"/>
+				<expand macro="hic_range_xml"/>
+			</when>
+			<when value="hic-normalize">
+		        <param format="h5" name="hic_project" type="data" label="HiFive HiC project file" optional="False"/>
+				<expand macro="hic_chromosomes_xml"/>
+				<expand macro="hic_range_xml"/>
+				<expand macro="hic_normalize_xml"/>
+			</when>
+			<when value="hic-heatmap">
+		        <param name="hic_project" type="data" format="h5" label="HiFive HiC project file" optional="False"/>
+				<expand macro="hic_chromosomes_xml"/>
+		        <param type="select" name="trans1" label="Calculate and include trans interactions">
+		            <option value="-t">yes</option>
+		            <option value="">no</option>
+		        </param>
+		        <expand macro="binsize_xml"/>
+		        <expand macro="hic_datatype_xml"/>
+		        <expand macro="dynamic_xml"/>
+		        <conditional name="image">
+		            <param name="generate" type="select" label="Generate image">
+		                <option value="yes">yes</option>
+		                <option value="no">no</option>
+		            </param>
+		            <when value="yes">
+		            	<expand macro="image_xml"/>
+		            </when>
+		            <when value="no"/>
+		        </conditional>
+			</when>
+			<when value="hic-interval">
+		        <param name="hic_project" type="data" format="h5" label="HiFive HiC project file" optional="False"/>
+		        <param type="text" name="chrom" size="10" label="Chromosome" optional="False">
+		            <validator type="empty_field" />
+		        </param>
+		        <param type="integer" name="start" value="0" label="Starting coordinate" optional="True">
+		            <validator type="in_range" min="0"/>
+		        </param>
+		        <param type="integer" name="stop" value="0" label="Stopping coordinate" optional="True">
+		            <validator type="in_range" min="0"/>
+		        </param>
+		        <expand macro="binsize_xml"/>
+		        <param type="integer" name="maxdist" value="0" label="Maximum interaction distance" optional="True" help="A value of zero will include all interaction distances that fall between the start and stop coordinates.">
+		            <validator type="in_range" min="0"/>
+		        </param>
+		        <expand macro="hic_datatype_xml"/>
+		        <expand macro="dynamic_xml"/>
+		        <conditional name="image">
+		            <param name="generate" type="select" label="Generate image">
+		                <option value="yes">yes</option>
+		                <option value="no">no</option>
+		            </param>
+		            <when value="yes">
+		            	<expand macro="image_xml"/>
+		            	<expand macro="rotate_xml"/>
+		            </when>
+		            <when value="no"/>
+		        </conditional>
+		    </when>
+			<when value="5c-complete">
+				<expand macro="5c_fragment_xml"/>
+				<expand macro="5c_sequence_xml"/>
+				<expand macro="5c_regions_xml"/>
+				<expand macro="5c_project_xml"/>
+				<expand macro="5c_range_xml"/>
+				<expand macro="5c_normalize_xml"/>
+			</when>
+			<when value="fragments">
+				<expand macro="5c_fragment_xml"/>
+			</when>
+			<when value="5c-data">
+		        <param format="h5" name="fragments" type="data" label="HiFive fragment file" optional="False"/>
+				<expand macro="5c_sequence_xml"/>
+			</when>
+			<when value="5c-project">
+		        <param format="h5" name="fivec_data" type="data" label="HiFive 5C data file" optional="False"/>
+				<expand macro="5c_regions_xml"/>
+				<expand macro="5c_project_xml"/>
+				<expand macro="5c_range_xml"/>
+			</when>
+			<when value="5c-normalize">
+		        <param format="h5" name="fivec_project" type="data" label="HiFive 5C project file" optional="False"/>
+				<expand macro="5c_regions_xml"/>
+				<expand macro="5c_range_xml"/>
+				<expand macro="5c_normalize_xml"/>
+			</when>
+			<when value="5c-heatmap">
+		        <param name="fivec_project" type="data" format="h5" label="HiFive 5C project file" optional="False"/>
+				<expand macro="5c_regions_xml"/>
+		        <param type="select" name="trans2" label="Calculate and include trans interactions">
+		            <option value="-t">yes</option>
+		            <option value="">no</option>
+		        </param>
+		        <expand macro="binsize_xml"/>
+		        <expand macro="5c_datatype_xml"/>
+		        <expand macro="dynamic_xml"/>
+		        <conditional name="image">
+		            <param name="generate" type="select" label="Generate image">
+		                <option value="yes">yes</option>
+		                <option value="no">no</option>
+		            </param>
+		            <when value="yes">
+		            	<expand macro="image_xml"/>
+		            </when>
+		            <when value="no"/>
+		        </conditional>
+			</when>
+			<when value="5c-interval">
+		        <param name="fivec_project" type="data" format="h5" label="HiFive 5C project file" optional="False"/>
+		        <param type="integer" name="region" value="" label="Region" optional="False">
+		            <validator type="empty_field" />
+		        </param>
+		        <param type="integer" name="start" value="0" label="Starting coordinate" optional="True">
+		            <validator type="in_range" min="0"/>
+		        </param>
+		        <param type="integer" name="stop" value="0" label="Stopping coordinate" optional="True">
+		            <validator type="in_range" min="0"/>
+		        </param>
+		        <expand macro="binsize_xml"/>
+		        <expand macro="5c_datatype_xml"/>
+		        <expand macro="dynamic_xml"/>
+		        <conditional name="image">
+		            <param name="generate" type="select" label="Generate image">
+		                <option value="yes">yes</option>
+		                <option value="no">no</option>
+		            </param>
+		            <when value="yes">
+		            	<expand macro="image_xml"/>
+		            	<expand macro="rotate_xml"/>
+		            </when>
+		            <when value="no"/>
+		        </conditional>
+		    </when>
+		</conditional>
+	</inputs>
+	<outputs>
+        <data format="h5" name="hic_comp_fends" label="${tool.name} on ${on_string}: HiC fends">
+        	<filter>(command["command_select"] == "hic-complete")</filter>
+        </data>
+        <data format="h5" name="hic_comp_data" label="${tool.name} on ${on_string}: HiC data">
+        	<filter>(command["command_select"] == "hic-complete")</filter>
+        </data>
+        <data format="h5" name="hic_comp_project" label="${tool.name} on ${on_string}: HiC project ${command.analysis.algorithm}">
+        	<filter>(command["command_select"] == "hic-complete")</filter>
+        </data>
+        <data format="h5" name="hic_fend_output" label="${tool.name} on ${on_string}: HiC fends">
+        	<filter>(command["command_select"] == "fends")</filter>
+        </data>
+        <data format="h5" name="hic_data_output" label="${tool.name} on ${on_string}: HiC data">
+        	<filter>(command["command_select"] == "hic-data")</filter>
+        </data>
+        <data format="h5" name="hic_project_output" label="${tool.name} on ${on_string}: HiC project">
+        	<filter>(command["command_select"] == "hic-project")</filter>
+        </data>
+        <data format="h5" name="hic_norm_output" label="${tool.name} on ${on_string}: HiC project ${command.analysis.algorithm}">
+        	<filter>(command["command_select"] == "hic-normalize")</filter>
+        </data>
+        <data format="h5" name="hic_hm_output" label="${tool.name} on ${on_string}: HiC heatmap HDF5">
+        	<filter>(command["command_select"] == "hic-heatmap")</filter>
+        </data>
+        <data format="png" name="hic_hm_image" label="${tool.name} on ${on_string}: HiC heatmap PNG">
+        	<filter>(command["command_select"] == "hic-heatmap")</filter>
+            <filter>(command["image"]["generate"] == "yes")</filter>
+        </data>
+        <data format="chrint" name="hic_int_output" label="${tool.name} on ${on_string}: HiC interval">
+        	<filter>(command["command_select"] == "hic-interval")</filter>
+        </data>
+        <data format="png" name="hic_int_image" label="${tool.name} on ${on_string}: HiC interval PNG">
+        	<filter>(command["command_select"] == "hic-interval")</filter>
+            <filter>(command["image"]["generate"] == "yes")</filter>
+        </data>
+        <data format="h5" name="fivec_comp_frags" label="${tool.name} on ${on_string}: 5C frags">
+        	<filter>(command["command_select"] == "5c-complete")</filter>
+        </data>
+        <data format="h5" name="fivec_comp_data" label="${tool.name} on ${on_string}: 5C data">
+        	<filter>(command["command_select"] == "5c-complete")</filter>
+        </data>
+        <data format="h5" name="fivec_comp_project" label="${tool.name} on ${on_string}: 5C project ${command.analysis.algorithm}">
+        	<filter>(command["command_select"] == "5c-complete")</filter>
+        </data>
+        <data format="h5" name="fivec_frag_output" label="${tool.name} on ${on_string}: 5C frags">
+        	<filter>(command["command_select"] == "fragments")</filter>
+        </data>
+        <data format="h5" name="fivec_data_output" label="${tool.name} on ${on_string}: 5C data">
+        	<filter>(command["command_select"] == "5c-data")</filter>
+        </data>
+        <data format="h5" name="fivec_project_output" label="${tool.name} on ${on_string}: 5C project">
+        	<filter>(command["command_select"] == "5c-project")</filter>
+        </data>
+        <data format="h5" name="fivec_norm_output" label="${tool.name} on ${on_string}: 5C project ${command.analysis.algorithm}">
+        	<filter>(command["command_select"] == "5c-normalize")</filter>
+        </data>
+        <data format="h5" name="fivec_hm_output" label="${tool.name} on ${on_string}: 5C heatmap HDF5">
+        	<filter>(command["command_select"] == "5c-heatmap")</filter>
+        </data>
+        <data format="png" name="fivec_hm_image" label="${tool.name} on ${on_string}: 5C heatmap PNG">
+        	<filter>(command["command_select"] == "5c-heatmap")</filter>
+            <filter>(command["image"]["generate"] == "yes")</filter>
+        </data>
+        <data format="chrint" name="fivec_int_output" label="${tool.name} on ${on_string}: 5C interval">
+        	<filter>(command["command_select"] == "5c-interval")</filter>
+        </data>
+        <data format="png" name="fivec_int_image" label="${tool.name} on ${on_string}: 5C interval PNG">
+        	<filter>(command["command_select"] == "5c-interval")</filter>
+            <filter>(command["image"]["generate"] == "yes")</filter>
+        </data>
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+@COMMAND_HELP@
+@HIC_HELP@
+@5C_HELP@
+]]></help>
+</tool>