Mercurial > repos > jdv > albacore
comparison albacore_1D.xml @ 2:b658298e65d8 draft
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
author | jdv |
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date | Fri, 08 Sep 2017 10:14:40 -0400 |
parents | 0a4f83207e53 |
children | 4d72adba794f |
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1:0a4f83207e53 | 2:b658298e65d8 |
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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 ${on_string} (reads)"> |
51 <filter>demux is True and out_format == 'fastq'</filter> | 51 <filter>demux is True and out_format == 'fastq'</filter> |
52 <discover_datasets pattern="(?P<name>.*)" directory="final" format="fastqsanger" /> | 52 <discover_datasets pattern="(?P<name>.*)" directory="final" format="fastqsanger" /> |
53 </collection> | 53 </collection> |
54 <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)"> | 54 <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)"> |
55 <filter>demux is True and out_format == 'fast5'</filter> | 55 <filter>demux is True and out_format == 'fast5'</filter> |
56 <discover_datasets pattern="(?P<name>.*)" directory="final" format="fast5_archive" /> | 56 <discover_datasets pattern="(?P<name>.*)" directory="final" format="fast5.tar.gz" /> |
57 </collection> | 57 </collection> |
58 <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${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 <!-- ***************************************************************** --> |