Mercurial > repos > jdv > albacore

comparison albacore_1D.xml @ 5:4d72adba794f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit aa6136c5fa32b987f64bd2b0dc1f72018038b0bb
author jdv
date Fri, 20 Oct 2017 23:10:23 -0400
parents b658298e65d8
children 3dfde840119e
comparison
equal deleted inserted replaced
4:8a9f61d08201 5:4d72adba794f
1 <tool id="albacore_1D" name="Albacore 1D" version="1.2.6"> 1 <tool id="albacore_1D" name="Albacore 1D" version="2.0.2">
2 2
3 <description>ONT production basecaller</description> 3 <description>ONT production basecaller</description>
4 4
5 <!-- ***************************************************************** --> 5 <!-- ***************************************************************** -->
6 6
32 <param name="out_format" type="select" label="Output format"> 32 <param name="out_format" type="select" label="Output format">
33 <option value="fastq" selected="true">fastq</option> 33 <option value="fastq" selected="true">fastq</option>
34 <option value="fast5">fast5</option> 34 <option value="fast5">fast5</option>
35 </param> 35 </param>
36 <param name="demux" type="boolean" checked="false" label="Demultiplex" /> 36 <param name="demux" type="boolean" checked="false" label="Demultiplex" />
37 <param name="output_table" type="boolean" checked="false" label="Include table in output" />
37 38
38 </inputs> 39 </inputs>
39 40
40 <!-- ***************************************************************** --> 41 <!-- ***************************************************************** -->
41 42
53 </collection> 54 </collection>
54 <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)"> 55 <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)">
55 <filter>demux is True and out_format == 'fast5'</filter> 56 <filter>demux is True and out_format == 'fast5'</filter>
56 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fast5.tar.gz" /> 57 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fast5.tar.gz" />
57 </collection> 58 </collection>
58 <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)" /> 59
60 <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)">
61 <filter>output_table is True</filter>
62 </data>
59 63
60 </outputs> 64 </outputs>
61 65
62 <!-- ***************************************************************** --> 66 <!-- ***************************************************************** -->
63 67
64 <tests> 68 <tests>
65 <test> 69 <test>
66 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" /> 70 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
67 <output name="output" file="test_data.fastq" compare="diff" /> 71 <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
68 </test> 72 </test>
69 </tests> 73 </tests>
70 74
71 <!-- ***************************************************************** --> 75 <!-- ***************************************************************** -->
72 76