Mercurial > repos > rnateam > graphclust_postprocessing
comparison glob_report.xml @ 5:fc701681ca6e draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
author | rnateam |
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date | Fri, 17 Mar 2017 08:23:26 -0400 |
parents | dbcea781900e |
children | 8d02b983f97a |
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4:dbcea781900e | 5:fc701681ca6e |
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1 <tool id="glob_report" name="cluster_collection_report" version="0.1"> | 1 <tool id="glob_report" name="cluster_collection_report" version="0.1"> |
2 <requirements> | 2 <requirements> |
3 <requirement type="package" version="0.1.10">graphclust-wrappers</requirement> | 3 <requirement type="package" version="0.1.11">graphclust-wrappers</requirement> |
4 <requirement type="package" version='0.5'>perl-array-utils</requirement> | 4 <requirement type="package" version='0.5'>perl-array-utils</requirement> |
5 <requirement type="package" version='0.18.1'>scikit-learn</requirement> | 5 <requirement type="package" version='0.18.1'>scikit-learn</requirement> |
6 <requirement type="package" version='1.8.10'>locarna</requirement> | 6 <requirement type="package" version='1.8.10'>locarna</requirement> |
7 <requirement type="package" version='2.1'>rnaz</requirement> | 7 <requirement type="package" version='2.1'>rnaz</requirement> |
8 <requirement type="package" version="1.1">infernal</requirement> | 8 <requirement type="package" version="1.1">infernal</requirement> |
45 $results_top_num | 45 $results_top_num |
46 #if $iteration_num.iteration_num_selector: | 46 #if $iteration_num.iteration_num_selector: |
47 $iteration_num.CI | 47 $iteration_num.CI |
48 $final_partition_soft | 48 $final_partition_soft |
49 $final_partition_used_cmsearch | 49 $final_partition_used_cmsearch |
50 '$combined_cm' | |
51 | |
50 #end if | 52 #end if |
51 | 53 |
52 #if str($advanced_opts.advanced_opts_selector) == "show": | 54 #if str($advanced_opts.advanced_opts_selector) == "show": |
53 #if str($advanced_opts.param_type.param_type_selector) == "gclust": | 55 #if str($advanced_opts.param_type.param_type_selector) == "gclust": |
54 $advanced_opts.param_type.p | 56 $advanced_opts.param_type.p |
81 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/> | 83 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/> |
82 <when value="true"> | 84 <when value="true"> |
83 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/> | 85 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/> |
84 <param type="data" name="final_partition_soft" format="txt" /> | 86 <param type="data" name="final_partition_soft" format="txt" /> |
85 <param type="data" name="final_partition_used_cmsearch" format="txt" /> | 87 <param type="data" name="final_partition_used_cmsearch" format="txt" /> |
88 <param type="data" name="combined_cm" format="txt" /> | |
86 </when> | 89 </when> |
87 <when value="false" ></when> | 90 <when value="false" ></when> |
88 </conditional> | 91 </conditional> |
89 <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/> | 92 <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/> |
90 <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/> | 93 <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/> |
141 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" /> | 144 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" /> |
142 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" /> | 145 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" /> |
143 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" /> | 146 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" /> |
144 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" /> | 147 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" /> |
145 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> | 148 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> |
149 <data name="combined_cm_out" format="txt" from_work_dir="combined_cmsearch_output" label="combined_cmsearch_output" /> | |
146 <collection name="clusters" type="list" label="CLUSTERS"> | 150 <collection name="clusters" type="list" label="CLUSTERS"> |
147 <discover_datasets pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> | 151 <discover_datasets pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> |
148 </collection> | 152 </collection> |
149 <collection name="partitions" type="list" label="Partitions"> | 153 <collection name="partitions" type="list" label="Partitions"> |
150 <discover_datasets pattern="(?P<name>^.*$)" directory="RESULTS/partitions" /> | 154 <discover_datasets pattern="(?P<name>^.*$)" directory="RESULTS/partitions" /> |