comparison hifive.xml @ 1:cb4f92e6fd4e draft

planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d

0:0a9c76d80e33

		@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@

				<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>

		            	<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"/>

        </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>

1:cb4f92e6fd4e

		@ROTATE@
		-i $hic_int_image
	#end if
	$hic_project $hic_int_output
#end if
#if str( $command.command_select ) == "hic-mrheatmap":
	@HIC_CHROMOSOMES@
	@HIC_DATATYPE@
	$command.trans1
	@MRH_OPTIONS@
	$hic_project $hic_mrheatmap
#end if
#if str( $command.command_select ) == "5c-complete":
	@5C_NORMALIZE@
	@5C_SEQUENCE@
	@5C_REGIONS@
	@5C_PROJECT@

				<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="hic-mrheatmap">Create HiC multi-resolution heatmap</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>

		            	<expand macro="rotate_xml"/>
		            </when>
		            <when value="no"/>
		        </conditional>
		    </when>
		   	<when value="hic-mrheatmap">
		        <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="mrh_options_xml"/>
		        <expand macro="hic_datatype_xml"/>
			</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"/>

        </data>
        <data format="png" name="hic_int_image" label="${tool.name} on ${on_string}: HiC interval PNG">
        	<filter>(command["command_select"] == "hic-interval")</filter>
            <filter>(command["image"]["generate"] == "yes")</filter>
        </data>
        <data format="mrh" name="hic_mrheatmap" label="${tool.name} on ${on_string}: HiC MR-heatmap">
        	<filter>(command["command_select"] == "hic-mrheatmap")</filter>
        </data>
        <data format="h5" name="fivec_comp_frags" label="${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>