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comparison glob_report.xml @ 4:4a9754d476fe draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0
author rnateam
date Fri, 13 Jan 2017 16:59:29 -0500
parents 79b9117aef01
children 4310ac018d05
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3:79b9117aef01 4:4a9754d476fe
1 <tool id="glob_report" name="Report_Results" version="0.1"> 1 <tool id="glob_report" name="Report_Results" version="0.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.1">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.1">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>
7 <requirement type="package" version='2.1'>rnaz</requirement>
8 <requirement type="package" version="1.1">infernal</requirement>
9 <requirement type="package" version='2.2.10'>viennarna</requirement>
10 <requirement type="package" version='1.3.23'>graphicsmagick</requirement>
6 </requirements> 11 </requirements>
7 <stdio> 12 <stdio>
8 <exit_code range="1:" /> 13 <exit_code range="1:" />
9 </stdio> 14 </stdio>
10 <command> 15 <command>
22 27
23 #for $mods in $model_tree_files: 28 #for $mods in $model_tree_files:
24 #set $inputFilesTrees += str($mods)+',' 29 #set $inputFilesTrees += str($mods)+','
25 #end for 30 #end for
26 #set $inputFilesTrees = $inputFilesTrees[:-1] 31 #set $inputFilesTrees = $inputFilesTrees[:-1]
27 glob_res.pl 32 glob_res.pl
28 '$inputFiles' 33 '$inputFiles'
29 $merge_cluster_ol 34 $merge_cluster_ol
30 $merge_overlap 35 $merge_overlap
31 $min_cluster_size 36 $min_cluster_size
32 $cm_min_bitscore 37 $cm_min_bitscore
33 $cm_max_eval 38 $cm_max_eval
34 $cm_bitscore_sig 39 $cm_bitscore_sig
35 $partition_type '' 40 $partition_type ''
36 $cut_type 41 $cut_type
37 '$inputFilesTrees' 42 '$inputFilesTrees'
43 $results_top_num
38 #if $iteration_num.iteration_num_selector: 44 #if $iteration_num.iteration_num_selector:
39 $iteration_num.CI 45 $iteration_num.CI
40 $final_partition_soft 46 $final_partition_soft
41 $final_partition_used_cmsearch 47 $final_partition_used_cmsearch
42 #end if 48 #end if
44 && 50 &&
45 python '$__tool_directory__/evaluation.py' 51 python '$__tool_directory__/evaluation.py'
46 #if $cdhit: 52 #if $cdhit:
47 && 53 &&
48 python '$__tool_directory__/addCdhitseqs.py' '$cdhit' 54 python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
49 #end if 55 #end if
50 ]]> 56 ]]>
51 </command> 57 </command>
52 <inputs> 58 <inputs>
53 <param type="data" name="FASTA" format="zip" /> 59 <param type="data" name="FASTA" format="zip" />
54 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/> 60 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/>
69 <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/> 75 <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/>
70 <param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/> 76 <param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/>
71 <param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/> 77 <param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/>
72 <param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/> 78 <param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/>
73 <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/> 79 <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/>
80 <param name="results_top_num" type="integer" value="5" size="5" label="results_top_num" help=""/>
74 </inputs> 81 </inputs>
75 <outputs> 82 <outputs>
76 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" /> 83 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" />
77 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" /> 84 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" />
78 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" /> 85 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" />
79 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" /> 86 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" />
80 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> 87 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" />
81 <collection name="clusters" type="list" label="CLUSTERS"> 88 <collection name="clusters" type="list" label="CLUSTERS">
82 <discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS" /> 89 <discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS" />
83 </collection> 90 </collection>
84 <collection name="partitions" type="list" label="Partitions"> 91 <collection name="partitions" type="list" label="Partitions">
85 <discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" /> 92 <discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" />
93 </collection>
94 <collection name="topSecondaryStruct" type="list" label="Top $results_top_num alirna.ps">
95 <discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.alirna.png$)" />
96 </collection>
97 <collection name="topDot" type="list" label="Top $results_top_num aln.ps">
98 <discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.aln.png$)" />
86 </collection> 99 </collection>
87 </outputs> 100 </outputs>
88 <tests> 101 <tests>
89 <test> 102 <test>
90 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> 103 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
123 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" /> 136 <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
124 <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" /> 137 <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
125 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" /> 138 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
126 <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/> 139 <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>
127 </output_collection> 140 </output_collection>
141 <param name="results_top_num" value="5"/>
142 <output_collection name="topSecondaryStruct" type="list">
143 <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
144 <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
145 </output_collection>
146 <output_collection name="topDot" type="list">
147 <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size"/>
148 <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size"/>
149 </output_collection>
128 </test> 150 </test>
129 </tests> 151 </tests>
130 <help> 152 <help>
131 <![CDATA[ 153 <![CDATA[
132 154