comparison glob_report.xml @ 4:4a9754d476fe draft

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0

3:79b9117aef01

<tool id="glob_report" name="Report_Results" version="0.1">
	<requirements>
		<requirement type="package" version="0.1">graphclust-wrappers</requirement>
		<requirement type="package" version='0.5'>perl-array-utils</requirement>
		<requirement type="package" version='0.18.1'>scikit-learn</requirement>
	</requirements>
	<stdio>
		<exit_code range="1:" />
	</stdio>
	<command>

        #for $mods in $model_tree_files:
            #set $inputFilesTrees += str($mods)+','
        #end for
        #set $inputFilesTrees = $inputFilesTrees[:-1]
		    glob_res.pl 
                '$inputFiles'
                $merge_cluster_ol
                $merge_overlap
                $min_cluster_size
                $cm_min_bitscore
                $cm_max_eval
                $cm_bitscore_sig
                $partition_type ''
                $cut_type
                '$inputFilesTrees'
        #if  $iteration_num.iteration_num_selector:
          $iteration_num.CI
          $final_partition_soft
          $final_partition_used_cmsearch
        #end if

        &&
        python '$__tool_directory__/evaluation.py'
		#if $cdhit:
    		&&
	    	python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
	    #end if		
]]>
	</command>
	<inputs>
		<param type="data" name="FASTA" format="zip" />
		<param type="data" name="cmsearch_results" format="tabular" multiple="True"/>

		<param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/>
		<param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/>
		<param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/>
		<param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/>
		<param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/>
	</inputs>
	<outputs>
		<data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats"  />
		<data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval"  />
		<data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part"   />
		<data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch"   />
		<data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters"   />
		<collection name="clusters" type="list" label="CLUSTERS">
			<discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS"  />
		</collection>
		<collection name="partitions" type="list" label="Partitions">
			<discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" />
		</collection>
	</outputs>
	<tests>
		<test>
			<param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>

				<element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
				<element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
				<element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
				<element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>
			</output_collection>
		</test>
	</tests>
	<help>
		<![CDATA[

4:4a9754d476fe

<tool id="glob_report" name="Report_Results" version="0.1">
	<requirements>
		<requirement type="package" version="0.1">graphclust-wrappers</requirement>
		<requirement type="package" version='0.5'>perl-array-utils</requirement>
		<requirement type="package" version='0.18.1'>scikit-learn</requirement>
		<requirement type="package" version='1.8.10'>locarna</requirement>
		<requirement type="package" version='2.1'>rnaz</requirement>
		<requirement type="package" version="1.1">infernal</requirement>
		<requirement type="package" version='2.2.10'>viennarna</requirement>
		<requirement type="package" version='1.3.23'>graphicsmagick</requirement>
	</requirements>
	<stdio>
		<exit_code range="1:" />
	</stdio>
	<command>

        #for $mods in $model_tree_files:
            #set $inputFilesTrees += str($mods)+','
        #end for
        #set $inputFilesTrees = $inputFilesTrees[:-1]
		    glob_res.pl
                '$inputFiles'
                $merge_cluster_ol
                $merge_overlap
                $min_cluster_size
                $cm_min_bitscore
                $cm_max_eval
                $cm_bitscore_sig
                $partition_type ''
                $cut_type
                '$inputFilesTrees'
                $results_top_num
        #if  $iteration_num.iteration_num_selector:
          $iteration_num.CI
          $final_partition_soft
          $final_partition_used_cmsearch
        #end if

        &&
        python '$__tool_directory__/evaluation.py'
		#if $cdhit:
    		&&
	    	python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
	    #end if
]]>
	</command>
	<inputs>
		<param type="data" name="FASTA" format="zip" />
		<param type="data" name="cmsearch_results" format="tabular" multiple="True"/>

		<param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/>
		<param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/>
		<param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/>
		<param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/>
		<param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/>
		<param name="results_top_num" type="integer" value="5" size="5" label="results_top_num" help=""/>
	</inputs>
	<outputs>
		<data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats"  />
		<data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval"  />
		<data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part"   />
		<data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch"   />
		<data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters"  />
		<collection name="clusters" type="list" label="CLUSTERS">
			<discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS"  />
		</collection>
		<collection name="partitions" type="list" label="Partitions">
			<discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" />
		</collection>
		<collection name="topSecondaryStruct" type="list" label="Top $results_top_num alirna.ps">
			<discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.alirna.png$)"  />
		</collection>
		<collection name="topDot" type="list" label="Top $results_top_num aln.ps">
			<discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.aln.png$)"  />
		</collection>
	</outputs>
	<tests>
		<test>
			<param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>

				<element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
				<element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
				<element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
				<element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>
			</output_collection>
			<param name="results_top_num" value="5"/>
			<output_collection name="topSecondaryStruct" type="list">
				<element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
				<element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
			</output_collection>
			<output_collection name="topDot" type="list">
				<element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png"  ftype="png" compare="sim_size"/>
				<element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png"  ftype="png" compare="sim_size"/>
			</output_collection>
		</test>
	</tests>
	<help>
		<![CDATA[