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comparison glob_report.xml @ 2:6c88ad83de28 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 16:57:54 -0500
parents 4503c49f31c4
children a8fde40f00fc
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1:e166d1382033 2:6c88ad83de28
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>
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>
5 </requirements> 11 </requirements>
6 <stdio> 12 <stdio>
7 <exit_code range="1:" /> 13 <exit_code range="1:" />
8 </stdio> 14 </stdio>
9 <command> 15 <command>
10 <![CDATA[ 16 <![CDATA[
11
12 unzip $FASTA &> /dev/null && 17 unzip $FASTA &> /dev/null &&
13 18
14 #set $inputFiles = "" 19 #set $inputFiles = ""
15 20
16 #for $cms_res in $cmsearch_results: 21 #for $cms_res in $cmsearch_results:
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 = $inputFilesTrees[:-1]
27 32 glob_res.pl
28 'glob_res.pl' '$inputFiles' $merge_cluster_ol $merge_overlap $min_cluster_size $cm_min_bitscore $cm_max_eval $cm_bitscore_sig $partition_type '' $cut_type '$inputFilesTrees' 33 '$inputFiles'
34 $merge_cluster_ol
35 $merge_overlap
36 $min_cluster_size
37 $cm_min_bitscore
38 $cm_max_eval
39 $cm_bitscore_sig
40 $partition_type ''
41 $cut_type
42 '$inputFilesTrees'
43 $results_top_num
29 #if $iteration_num.iteration_num_selector: 44 #if $iteration_num.iteration_num_selector:
30 $iteration_num.CI 45 $iteration_num.CI
31
32 $final_partition_soft 46 $final_partition_soft
33 $final_partition_used_cmsearch 47 $final_partition_used_cmsearch
34 #end if 48 #end if
35 49
36 && 50 &&
37 python '$__tool_directory__/evaluation.py' 51 python '$__tool_directory__/evaluation.py'
52 #if $cdhit:
53 &&
54 python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
55 #end if
38 ]]> 56 ]]>
39 </command> 57 </command>
40 <inputs> 58 <inputs>
41 <param type="data" name="FASTA" format="zip" /> 59 <param type="data" name="FASTA" format="zip" />
42 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/> 60 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/>
43 <param type="data" name="model_tree_files" format="txt" multiple="True"/> 61 <param type="data" name="model_tree_files" format="txt" multiple="True"/>
44 <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/> 62 <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>
45 <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/> 63 <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
64 <param type="data" name="cdhit" format="txt" optional="true"/>
46 <conditional name="iteration_num"> 65 <conditional name="iteration_num">
47 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/> 66 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>
48 <when value="true"> 67 <when value="true">
49 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/> 68 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
50 <param type="data" name="final_partition_soft" format="txt" /> 69 <param type="data" name="final_partition_soft" format="txt" />
56 <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=""/>
57 <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=""/>
58 <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=""/>
59 <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=""/>
60 <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=""/>
61 </inputs> 81 </inputs>
62 <outputs> 82 <outputs>
63 <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" />
64 <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" />
65 <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" />
66 <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" />
87 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" />
67 <collection name="clusters" type="list" label="CLUSTERS"> 88 <collection name="clusters" type="list" label="CLUSTERS">
68 <discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS" /> 89 <discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS" />
69 </collection> 90 </collection>
70 <collection name="partitions" type="list" label="Partitions"> 91 <collection name="partitions" type="list" label="Partitions">
71 <discover_datasets pattern="(?P&lt;name&gt;^.*$)" 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 $results_top_num aln.ps">
98 <discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.aln.png$)" />
72 </collection> 99 </collection>
73 </outputs> 100 </outputs>
74 <tests> 101 <tests>
75 <test> 102 <test>
76 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> 103 <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
109 <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" />
110 <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" />
111 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" /> 138 <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
112 <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"/>
113 </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>
114 </test> 150 </test>
115 </tests> 151 </tests>
116 <help> 152 <help>
117 <![CDATA[ 153 <![CDATA[
118 154