Mercurial > repos > jdv > albacore

comparison albacore_1D.xml @ 2:b658298e65d8 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
author jdv
date Fri, 08 Sep 2017 10:14:40 -0400
parents 0a4f83207e53
children 4d72adba794f
comparison
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1:0a4f83207e53 2:b658298e65d8
26 26
27 <!-- ***************************************************************** --> 27 <!-- ***************************************************************** -->
28 28
29 <inputs> 29 <inputs>
30 30
31 <param name="input" type="data" format="fast5_archive" label="Input reads" /> 31 <param name="input" type="data" format="fast5.tar" label="Input reads" />
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" />
42 <outputs> 42 <outputs>
43 43
44 <data name="output" format="fastq" label="${tool.name} on ${on_string} (reads)"> 44 <data name="output" format="fastq" label="${tool.name} on ${on_string} (reads)">
45 <filter>demux is False</filter> 45 <filter>demux is False</filter>
46 <change_format> 46 <change_format>
47 <when input="out_format" value="fast5" format="fast5_archive" /> 47 <when input="out_format" value="fast5" format="fast5.tar.gz" />
48 </change_format> 48 </change_format>
49 </data> 49 </data>
50 <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string} (reads)"> 50 <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string} (reads)">
51 <filter>demux is True and out_format == 'fastq'</filter> 51 <filter>demux is True and out_format == 'fastq'</filter>
52 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fastqsanger" /> 52 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fastqsanger" />
53 </collection> 53 </collection>
54 <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)"> 54 <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)">
55 <filter>demux is True and out_format == 'fast5'</filter> 55 <filter>demux is True and out_format == 'fast5'</filter>
56 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fast5_archive" /> 56 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fast5.tar.gz" />
57 </collection> 57 </collection>
58 <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)" /> 58 <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)" />
59 59
60 </outputs> 60 </outputs>
61 61
62 <!-- ***************************************************************** --> 62 <!-- ***************************************************************** -->
63 63
64 <tests> 64 <tests>
65 <test> 65 <test>
66 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" /> 66 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
67 <output name="output" file="test_data.fastq" compare="diff" /> 67 <output name="output" file="test_data.fastq" compare="diff" />
68 </test> 68 </test>
69 </tests> 69 </tests>
70 70
71 <!-- ***************************************************************** --> 71 <!-- ***************************************************************** -->