Mercurial > repos > iuc > nanopolishcomp_eventaligncollapse

comparison eventaligncollapse.xml @ 1:ad011fc670d6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
author iuc
date Tue, 12 May 2020 17:08:45 -0400
parents 6847a625db4d
children 74d7b06c2b92
comparison
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0:6847a625db4d 1:ad011fc670d6
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="nanopolishcomp_eventaligncollapse" name="Eventalign Collapse" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> 2 <tool id="nanopolishcomp_eventaligncollapse" name="NanopolishComp: EventalignCollapse" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
3 <description>by kmers rather than by event</description> 3 <description>by kmers rather than by event</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <stdio></stdio> 8 <expand macro="version_command"/>
9 <version_command>NanopolishComp --version</version_command>
10 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
11 ## initialize 10 ## initialize
12 ## requires a minimum of 3 threads 11 ## requires a minimum of 3 threads
13 threads=\$((3 > \${GALAXY_SLOTS:-3} ? 3 : \${GALAXY_SLOTS:-3})) && 12 threads=\$((3 > \${GALAXY_SLOTS:-3} ? 3 : \${GALAXY_SLOTS:-3})) &&
14 13
16 NanopolishComp 15 NanopolishComp
17 Eventalign_collapse 16 Eventalign_collapse
18 -i '$i' 17 -i '$i'
19 -s 18 -s
20 -r $r 19 -r $r
21 -f 20 -f
22 #for $current in $f 21 #for $current in $f
23 $current 22 $current
24 #end for 23 #end for
25 -o 'results' 24 -o 'results'
26 -p 'out' 25 -p 'out'
27 -t \$threads 26 -t \$threads
28 -v 27 -v
36 <option value="std">Std</option> 35 <option value="std">Std</option>
37 <option value="median" selected="true">Median</option> 36 <option value="median" selected="true">Median</option>
38 <option value="mad">Mad</option> 37 <option value="mad">Mad</option>
39 <option value="num_signals" selected="true">Number of signals</option> 38 <option value="num_signals" selected="true">Number of signals</option>
40 </param> 39 </param>
41 <param name="out" type="select" multiple="true" label="Select output file(s)" help=""> 40 <param name="out" type="select" multiple="true" label="Select output file(s)">
42 <option value="eventalign_collapse" selected="true">Eventalign Collapse</option> 41 <option value="eventalign_collapse" selected="true">Eventalign Collapse</option>
43 <option value="index" selected="true">Index</option> 42 <option value="index" selected="true">Index</option>
44 <option value="log">Log</option> 43 <option value="log">Log</option>
45 </param> 44 </param>
46 </inputs> 45 </inputs>
49 <filter>'eventalign_collapse' in out</filter> 48 <filter>'eventalign_collapse' in out</filter>
50 </data> 49 </data>
51 <data name="out_index" format="tabular" from_work_dir="results/out_eventalign_collapse.tsv.idx" label="${tool.name} on ${on_string}: Index"> 50 <data name="out_index" format="tabular" from_work_dir="results/out_eventalign_collapse.tsv.idx" label="${tool.name} on ${on_string}: Index">
52 <filter>'index' in out</filter> 51 <filter>'index' in out</filter>
53 </data> 52 </data>
54 <data name="out_log" format="txt" from_work_dir="results/out_eventalign_collapse.log" label="${tool.name} on ${on_string}: log"> 53 <data name="out_log" format="txt" from_work_dir="results/out_eventalign_collapse.log" label="${tool.name} on ${on_string}: Log">
55 <filter>'log' in out</filter> 54 <filter>'log' in out</filter>
56 </data> 55 </data>
57 </outputs> 56 </outputs>
58 <tests> 57 <tests>
59 <!-- #1 default --> 58 <!-- #1 default -->
60 <test expect_num_outputs="3"> 59 <test expect_num_outputs="3">
61 <param name="i" value="sample.tsv"/> 60 <param name="i" value="sample_event.tsv"/>
62 <param name="out" value="eventalign_collapse,index,log"/> 61 <param name="out" value="eventalign_collapse,index,log"/>
63 <output name="out_eventalign_collapse"> 62 <output name="out_eventalign_collapse">
64 <assert_contents> 63 <assert_contents>
65 <has_n_lines n="236"/> 64 <has_n_lines n="236"/>
66 <has_text_matching expression="ref_pos&#009;ref_kmer"/> 65 <has_text_matching expression="ref_pos&#009;ref_kmer"/>
81 </assert_contents> 80 </assert_contents>
82 </output> 81 </output>
83 </test> 82 </test>
84 <!-- #2 --> 83 <!-- #2 -->
85 <test expect_num_outputs="2"> 84 <test expect_num_outputs="2">
86 <param name="i" value="sample.tsv"/> 85 <param name="i" value="sample_event.tsv"/>
87 <param name="s" value="true"/> 86 <param name="s" value="true"/>
88 <param name="r" value="10"/> 87 <param name="r" value="10"/>
89 <param name="f" value="mean,std,median,mad,num_signals"/> 88 <param name="f" value="mean,std,median,mad,num_signals"/>
90 <param name="out" value="eventalign_collapse,index"/> 89 <param name="out" value="eventalign_collapse,index"/>
91 <output name="out_eventalign_collapse"> 90 <output name="out_eventalign_collapse">
113 112
114 Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. 113 Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event.
115 114
116 **Input** 115 **Input**
117 116
118 A nanopolish eventalign tabular output file. 117 A nanopolish eventalign tabular output file.
119 118
120 **Output** 119 **Output**
121 120
122 Contrary to nanopolish eventalign output text file, in Eventalign_collapse the reads are separated by a hashtag headers containing the read_id and ref_id. This reduces the redundancy and makes it easier to find the start and end of a read. 121 Contrary to nanopolish eventalign output text file, in Eventalign_collapse the reads are separated by a hashtag headers containing the read_id and ref_id. This reduces the redundancy and makes it easier to find the start and end of a read.
123 122