| Previous changeset 4:4a9754d476fe (2017-01-13) Next changeset 6:869a6e807d76 (2017-02-22) |
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Commit message:
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 |
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modified:
evaluation.py glob_report.xml |
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added:
test-data/RESULTS.zip |
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| diff -r 4a9754d476fe -r 4310ac018d05 evaluation.py --- a/evaluation.py Fri Jan 13 16:59:29 2017 -0500 +++ b/evaluation.py Sat Jan 21 17:39:21 2017 -0500 |
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| @@ -2,6 +2,7 @@ from os import system import re from sklearn import metrics +from shutil import make_archive def sh(script): system("bash -c '%s'" % script) @@ -67,3 +68,6 @@ with open("RESULTS/evaluation.txt", "w") as fOut: fOut.write(toWrite) + + +make_archive('RESULTS', 'zip', root_dir='RESULTS') |
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| diff -r 4a9754d476fe -r 4310ac018d05 glob_report.xml --- a/glob_report.xml Fri Jan 13 16:59:29 2017 -0500 +++ b/glob_report.xml Sat Jan 21 17:39:21 2017 -0500 |
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| b'@@ -1,19 +1,19 @@\n <tool id="glob_report" name="Report_Results" version="0.1">\n-\t<requirements>\n-\t\t<requirement type="package" version="0.1">graphclust-wrappers</requirement>\n-\t\t<requirement type="package" version=\'0.5\'>perl-array-utils</requirement>\n-\t\t<requirement type="package" version=\'0.18.1\'>scikit-learn</requirement>\n-\t\t<requirement type="package" version=\'1.8.10\'>locarna</requirement>\n-\t\t<requirement type="package" version=\'2.1\'>rnaz</requirement>\n-\t\t<requirement type="package" version="1.1">infernal</requirement>\n-\t\t<requirement type="package" version=\'2.2.10\'>viennarna</requirement>\n-\t\t<requirement type="package" version=\'1.3.23\'>graphicsmagick</requirement>\n-\t</requirements>\n-\t<stdio>\n-\t\t<exit_code range="1:" />\n-\t</stdio>\n-\t<command>\n-\t\t<![CDATA[\n+ <requirements>\n+ <requirement type="package" version="0.1.7">graphclust-wrappers</requirement>\n+ <requirement type="package" version=\'0.5\'>perl-array-utils</requirement>\n+ <requirement type="package" version=\'0.18.1\'>scikit-learn</requirement>\n+ <requirement type="package" version=\'1.8.10\'>locarna</requirement>\n+ <requirement type="package" version=\'2.1\'>rnaz</requirement>\n+ <requirement type="package" version="1.1">infernal</requirement>\n+ <requirement type="package" version=\'2.2.10\'>viennarna</requirement>\n+ <requirement type="package" version=\'1.3.23\'>graphicsmagick</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command>\n+ <![CDATA[\n unzip $FASTA &> /dev/null &&\n \n #set $inputFiles = ""\n@@ -29,7 +29,7 @@\n #set $inputFilesTrees += str($mods)+\',\'\n #end for\n #set $inputFilesTrees = $inputFilesTrees[:-1]\n-\t\t glob_res.pl\n+ \'glob_res.pl\'\n \'$inputFiles\'\n $merge_cluster_ol\n $merge_overlap\n@@ -47,110 +47,169 @@\n $final_partition_used_cmsearch\n #end if\n \n+ #if str($advanced_opts.advanced_opts_selector) == "show":\n+ #if str($advanced_opts.param_type.param_type_selector) == "gclust":\n+ $advanced_opts.param_type.p\n+ $advanced_opts.param_type.max_diff_am\n+ $advanced_opts.param_type.max_diff\n+ $advanced_opts.param_type.tau\n+ $advanced_opts.param_type.struct_weight\n+ $advanced_opts.param_type.indel_opening\n+ $advanced_opts.param_type.indel\n+ $advanced_opts.param_type.alifold_consensus_dp\n+ #end if\n+ #end if\n+\n &&\n python \'$__tool_directory__/evaluation.py\'\n-\t\t#if $cdhit:\n- \t\t&&\n-\t \tpython \'$__tool_directory__/addCdhitseqs.py\' \'$cdhit\'\n-\t #end if\n+ #if $cdhit:\n+ &&\n+ python \'$__tool_directory__/addCdhitseqs.py\' \'$cdhit\'\n+ #end if\n ]]>\n-\t</command>\n-\t<inputs>\n-\t\t<param type="data" name="FASTA" format="zip" />\n-\t\t<param type="data" name="cmsearch_results" format="tabular" multiple="True"/>\n-\t\t<param type="data" name="model_tree_files" format="txt" multiple="True"/>\n-\t\t<param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>\n-\t\t<param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>\n-\t\t<param type="data" name="cdhit" format="txt" optional="true"/>\n-\t\t<conditional name="iteration_num">\n-\t\t\t<param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>\n-\t\t\t<when value="true">\n-\t\t\t\t<param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>\n-\t\t\t\t<param type="data" name="final_partition_soft" format="txt" />\n-\t\t\t\t<param type="data" name="final_partition_used_cmsearch" format="txt" />\n-\t\t\t</when>\n-\t\t\t<when value="false" ></when>\n-\t\t</conditional>\n-\t\t<param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_clust'..b'pe="list" label="Partitions">\n+ <discover_datasets pattern="(?P<name>^.*$)" directory="RESULTS/partitions" />\n+ </collection>\n+ <collection name="topSecondaryStruct" type="list" label="Top $results_top_num alirna.ps">\n+ <discover_datasets format="png" pattern="(?P<name>^.*\\.alirna.png$)" />\n+ </collection>\n+ <collection name="topDot" type="list" label="Top $results_top_num aln.ps">\n+ <discover_datasets format="png" pattern="(?P<name>^.*\\.aln.png$)" />\n+ </collection>\n+ <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>\n+ <param name="cmsearch_results" value="1.tabular,2.tabular"/>\n+ <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>\n+ <param name="partition_type" value="0"/>\n+ <param name="cut_type" value="0"/>\n+ <conditional name="iteration_num">\n+ <param name="iteration_num_selector" value="false"/>\n+ </conditional>\n+ <param name="merge_cluster_ol" value="0.66"/>\n+ <param name="merge_overlap" value="0.51"/>\n+ <param name="min_cluster_size" value="3"/>\n+ <param name="cm_min_bitscore" value="20"/>\n+ <param name="cm_max_eval" value="0.001"/>\n+ <param name="cm_bitscore_sig" value="1"/>\n+ <output name="final_stats" file="RESULTS/cluster.final.stats" />\n+ <output_collection name="clusters" type="list">\n+ <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>\n+ <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>\n+ </output_collection>\n+ <output_collection name="partitions">\n+ <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">\n+ <assert_contents>\n+ <has_text text="1.1 1.1" />\n+ <has_text text="1.2 1.2" />\n+ </assert_contents>\n+ </element>\n+ <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">\n+ <assert_contents>\n+ <has_text text="MODEL CLASS 0 0" />\n+ <has_text text="1.2" />\n+ <has_text text="1.1" />\n+ </assert_contents>\n+ </element>\n+ <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />\n+ <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />\n+ <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />\n+ <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>\n+ </output_collection>\n+ <param name="results_top_num" value="5"/>\n+ <output_collection name="topSecondaryStruct" type="list">\n+ <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" />\n+ <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" />\n+ </output_collection>\n+ <output_collection name="topDot" type="list">\n+ <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size" />\n+ <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size" />\n+ </output_collection>\n+ <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" />\n+\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n \n **What it does**\n \n@@ -160,8 +219,8 @@\n Cluster members are finally ranked by their CM bitscore.\n \n ]]>\n-\t</help>\n-\t<citations>\n+ </help>\n+ <citations>\n <citation type="bibtex">@inproceedings{costa2010fast,\n title={Fast neighborhood subgraph pairwise distance kernel},\n author={Costa, Fabrizio and De Grave, Kurt},\n' |
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| diff -r 4a9754d476fe -r 4310ac018d05 test-data/RESULTS.zip |
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| Binary file test-data/RESULTS.zip has changed |