Mercurial > repos > iuc > nanopolishcomp_eventaligncollapse
comparison eventaligncollapse.xml @ 1:ad011fc670d6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ commit cc7e6263fdb9e59f992aee41fc9d62425f39bf38"
author | iuc |
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date | Tue, 12 May 2020 17:08:45 -0400 |
parents | 6847a625db4d |
children | 74d7b06c2b92 |
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0:6847a625db4d | 1:ad011fc670d6 |
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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	ref_kmer"/> | 65 <has_text_matching expression="ref_pos	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 |