Mercurial > repos > rnateam > graphclust_postprocessing

comparison glob_report.xml @ 6:8d02b983f97a draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 4dd7269185f6fb9bdc007028007d6540f4cf057d
author rnateam
date Sat, 25 Mar 2017 16:33:54 -0400
parents fc701681ca6e
children 911e58500508
comparison
equal deleted inserted replaced
5:fc701681ca6e 6:8d02b983f97a
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="0.1.11">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.1.12">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>
16 </stdio> 16 </stdio>
17 <command> 17 <command>
18 <![CDATA[ 18 <![CDATA[
19 unzip $FASTA &> /dev/null && 19 unzip $FASTA &> /dev/null &&
20 20
21 mkdir ./CMSEARCH &&
22 mkdir ./MODEL &&
23
21 #set $inputFiles = "" 24 #set $inputFiles = ""
22 25
23 #for $cms_res in $cmsearch_results: 26 #for $cms_res in $cmsearch_results:
24 #set $inputFiles += str($cms_res)+',' 27 ###set $inputFiles += str($cms_res.element_identifier)+','
28 ln -f -s '$cms_res' ./CMSEARCH/$cms_res.element_identifier &&
25 #end for 29 #end for
26 #set $inputFiles = $inputFiles[:-1] 30 #set $inputFiles = $inputFiles[:-1]
27 31
28 #set $inputFilesTrees = "" 32 #set $inputFilesTrees = ""
29 33
30 #for $mods in $model_tree_files: 34 #for $mods in $model_tree_files:
31 #set $inputFilesTrees += str($mods)+',' 35 ###set $inputFilesTrees += str($mods.element_identifier)+','
36 ln -f -s '$mods' ./MODEL/$mods.element_identifier &&
32 #end for 37 #end for
33 #set $inputFilesTrees = $inputFilesTrees[:-1] 38 #set $inputFilesTrees = $inputFilesTrees[:-1]
34 'glob_res.pl' 39 'glob_res.pl'
35 '$inputFiles' 40 ##'$inputFiles'
36 $merge_cluster_ol 41 $merge_cluster_ol
37 $merge_overlap 42 $merge_overlap
38 $min_cluster_size 43 $min_cluster_size
39 $cm_min_bitscore 44 $cm_min_bitscore
40 $cm_max_eval 45 $cm_max_eval
41 $cm_bitscore_sig 46 $cm_bitscore_sig
42 $partition_type '' 47 $partition_type ''
43 $cut_type 48 $cut_type
44 '$inputFilesTrees' 49 ##'$inputFilesTrees'
45 $results_top_num 50 $results_top_num
46 #if $iteration_num.iteration_num_selector: 51 #if $iteration_num.iteration_num_selector:
47 $iteration_num.CI 52 $iteration_num.CI
48 $final_partition_soft 53 $final_partition_soft
49 $final_partition_used_cmsearch 54 $final_partition_used_cmsearch
144 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" /> 149 <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" />
145 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" /> 150 <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" />
146 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" /> 151 <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" />
147 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" /> 152 <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" />
148 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> 153 <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" />
149 <data name="combined_cm_out" format="txt" from_work_dir="combined_cmsearch_output" label="combined_cmsearch_output" /> 154 <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output" />
150 <collection name="clusters" type="list" label="CLUSTERS"> 155 <collection name="clusters" type="list" label="CLUSTERS">
151 <discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS" /> 156 <discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS" />
152 </collection> 157 </collection>
153 <collection name="partitions" type="list" label="Partitions"> 158 <collection name="partitions" type="list" label="Partitions">
154 <discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" /> 159 <discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" />