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comparison albacore_1D.xml @ 8:3dfde840119e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
author jdv
date Mon, 18 Jun 2018 12:20:28 -0400
parents 4d72adba794f
children
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7:ce1fa05ffb6c 8:3dfde840119e
1 <tool id="albacore_1D" name="Albacore 1D" version="2.0.2"> 1 <tool id="albacore_1D" name="Albacore 1D" version="2.0.2b">
2 2
3 <description>ONT production basecaller</description> 3 <description>ONT production basecaller</description>
4 4
5 <!-- ***************************************************************** --> 5 <!-- ***************************************************************** -->
6 6
7 <!-- 7 <!--
8 <requirements> 8 <requirements>
9 <requirement type="package" version="1.2.6">albacore</requirement> 9 <requirement type="package" version="2.0.2">albacore</requirement>
10 </requirements> 10 </requirements>
11 --> 11 -->
12 12
13 <!-- ***************************************************************** --> 13 <!-- ***************************************************************** -->
14 14
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 $out_format $demux \${GALAXY_SLOTS:-1} 22 python3 $__tool_directory__/albacore_1D.py $input $output $out_format $demux $disable_filt \${GALAXY_SLOTS:-1}
23 23
24 ]]> 24 ]]>
25 </command> 25 </command>
26 26
27 <!-- ***************************************************************** --> 27 <!-- ***************************************************************** -->
32 <param name="out_format" type="select" label="Output format"> 32 <param name="out_format" type="select" label="Output format">
33 <option value="fastq" selected="true">fastq</option> 33 <option value="fastq" selected="true">fastq</option>
34 <option value="fast5">fast5</option> 34 <option value="fast5">fast5</option>
35 </param> 35 </param>
36 <param name="demux" type="boolean" checked="false" label="Demultiplex" /> 36 <param name="demux" type="boolean" checked="false" label="Demultiplex" />
37 <param name="disable_filt" type="boolean" checked="false" label="Disable quality filtering" />
37 <param name="output_table" type="boolean" checked="false" label="Include table in output" /> 38 <param name="output_table" type="boolean" checked="false" label="Include table in output" />
38 39
39 </inputs> 40 </inputs>
40 41
41 <!-- ***************************************************************** --> 42 <!-- ***************************************************************** -->
54 </collection> 55 </collection>
55 <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)"> 56 <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)">
56 <filter>demux is True and out_format == 'fast5'</filter> 57 <filter>demux is True and out_format == 'fast5'</filter>
57 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fast5.tar.gz" /> 58 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="final" format="fast5.tar.gz" />
58 </collection> 59 </collection>
59
60 <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)"> 60 <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)">
61 <filter>output_table is True</filter> 61 <filter>output_table is True</filter>
62 </data> 62 </data>
63 63
64 </outputs> 64 </outputs>
67 67
68 <tests> 68 <tests>
69 <test> 69 <test>
70 <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" />
71 <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/> 71 <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
72 </test>
73 <test>
74 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" />
75 <param name="disable_filt" value="true" />
76 <output name="output" file="test_data_nofilt.fastq" compare="sim_size" delta="0"/>
72 </test> 77 </test>
73 </tests> 78 </tests>
74 79
75 <!-- ***************************************************************** --> 80 <!-- ***************************************************************** -->
76 81