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comparison albacore_1D.xml @ 1:0a4f83207e53 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 4aa7a76a7b29c425dd89a020979e835d785d3c95-dirty
author jdv
date Wed, 06 Sep 2017 12:12:52 -0400
parents f8e25d69167d
children b658298e65d8
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0:f8e25d69167d 1:0a4f83207e53
17 <!-- ***************************************************************** --> 17 <!-- ***************************************************************** -->
18 18
19 <command detect_errors="aggressive"> 19 <command detect_errors="aggressive">
20 <![CDATA[ 20 <![CDATA[
21 21
22 python3 $__tool_directory__/albacore_1D.py $input $output \${GALAXY_SLOTS:-1} 22 python3 $__tool_directory__/albacore_1D.py $input $output $out_format $demux \${GALAXY_SLOTS:-1}
23 23
24 ]]> 24 ]]>
25 </command> 25 </command>
26 26
27 <!-- ***************************************************************** --> 27 <!-- ***************************************************************** -->
28 28
29 <inputs> 29 <inputs>
30 30
31 <param name="input" type="data" format="fast5_archive" label="Input reads" /> 31 <param name="input" type="data" format="fast5_archive" label="Input reads" />
32 <param name="out_format" type="select" label="Output format">
33 <option value="fastq" selected="true">fastq</option>
34 <option value="fast5">fast5</option>
35 </param>
36 <param name="demux" type="boolean" checked="false" label="Demultiplex" />
32 37
33 </inputs> 38 </inputs>
34 39
35 <!-- ***************************************************************** --> 40 <!-- ***************************************************************** -->
36 41
37 <outputs> 42 <outputs>
38 43
39 <data name="output" format="fastq" label="${tool.name} on ${on_string} (called.fastq)" /> 44 <data name="output" format="fastq" label="${tool.name} on ${on_string} (reads)">
45 <filter>demux is False</filter>
46 <change_format>
47 <when input="out_format" value="fast5" format="fast5_archive" />
48 </change_format>
49 </data>
50 <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string} (reads)">
51 <filter>demux is True and out_format == 'fastq'</filter>
52 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fastqsanger" />
53 </collection>
54 <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)">
55 <filter>demux is True and out_format == 'fast5'</filter>
56 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fast5_archive" />
57 </collection>
58 <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)" />
40 59
41 </outputs> 60 </outputs>
42 61
43 <!-- ***************************************************************** --> 62 <!-- ***************************************************************** -->
44 63