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comparison glob_report.xml @ 3:79b9117aef01 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
author rnateam
date Wed, 04 Jan 2017 18:15:07 -0500
parents b8e32e577597
children 4a9754d476fe
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2:b8e32e577597 3:79b9117aef01
7 <stdio> 7 <stdio>
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 </stdio> 9 </stdio>
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12
13 unzip $FASTA &> /dev/null && 12 unzip $FASTA &> /dev/null &&
14 13
15 #set $inputFiles = "" 14 #set $inputFiles = ""
16 15
17 #for $cms_res in $cmsearch_results: 16 #for $cms_res in $cmsearch_results:
23 22
24 #for $mods in $model_tree_files: 23 #for $mods in $model_tree_files:
25 #set $inputFilesTrees += str($mods)+',' 24 #set $inputFilesTrees += str($mods)+','
26 #end for 25 #end for
27 #set $inputFilesTrees = $inputFilesTrees[:-1] 26 #set $inputFilesTrees = $inputFilesTrees[:-1]
28 27 glob_res.pl
29 'glob_res.pl' '$inputFiles' $merge_cluster_ol $merge_overlap $min_cluster_size $cm_min_bitscore $cm_max_eval $cm_bitscore_sig $partition_type '' $cut_type '$inputFilesTrees' 28 '$inputFiles'
29 $merge_cluster_ol
30 $merge_overlap
31 $min_cluster_size
32 $cm_min_bitscore
33 $cm_max_eval
34 $cm_bitscore_sig
35 $partition_type ''
36 $cut_type
37 '$inputFilesTrees'
30 #if $iteration_num.iteration_num_selector: 38 #if $iteration_num.iteration_num_selector:
31 $iteration_num.CI 39 $iteration_num.CI
32
33 $final_partition_soft 40 $final_partition_soft
34 $final_partition_used_cmsearch 41 $final_partition_used_cmsearch
35 #end if 42 #end if
36 43
37 && 44 &&
38 python '$__tool_directory__/evaluation.py' 45 python '$__tool_directory__/evaluation.py'
46 #if $cdhit:
47 &&
48 python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
49 #end if
39 ]]> 50 ]]>
40 </command> 51 </command>
41 <inputs> 52 <inputs>
42 <param type="data" name="FASTA" format="zip" /> 53 <param type="data" name="FASTA" format="zip" />
43 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/> 54 <param type="data" name="cmsearch_results" format="tabular" multiple="True"/>
44 <param type="data" name="model_tree_files" format="txt" multiple="True"/> 55 <param type="data" name="model_tree_files" format="txt" multiple="True"/>
45 <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/> 56 <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>
46 <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/> 57 <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
58 <param type="data" name="cdhit" format="txt" optional="true"/>
47 <conditional name="iteration_num"> 59 <conditional name="iteration_num">
48 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/> 60 <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/>
49 <when value="true"> 61 <when value="true">
50 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/> 62 <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
51 <param type="data" name="final_partition_soft" format="txt" /> 63 <param type="data" name="final_partition_soft" format="txt" />