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comparison macs2_randsample.xml @ 5:beb902da6e5f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
author iuc
date Sat, 08 Apr 2017 08:28:57 -0400
parents bfe57d6e0c4c
children acbd3fb47f90
comparison
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4:56e104999978 5:beb902da6e5f
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command>
10 <![CDATA[
10 macs2 randsample 11 macs2 randsample
11 -t "${ infile }" 12 -t '${ infile }'
12 -o "${ outfile }" 13 -o '${ outfile }'
14 --seed '${ seed }'
13 15
14 --format '${ infile.extension.upper() }' 16 --format '${ infile.extension.upper() }'
15 17
16 @tag_size@ 18 @tag_size@
19
17 #if $method_options.method_options_selector == 'percentage': 20 #if $method_options.method_options_selector == 'percentage':
18 --percentage "${ method_options.percentage }" 21 --percentage '${ method_options.percentage }'
19 #else: 22 #else:
20 --number "${ method_options.number }" 23 --number '${ method_options.number }'
21 #end if 24 #end if
25 ]]>
22 </command> 26 </command>
23 <inputs> 27 <inputs>
24 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> 28 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
25 <expand macro="tag_size" /> 29 <expand macro="tag_size" />
26
27 <conditional name="method_options"> 30 <conditional name="method_options">
28 <param name="method_options_selector" type="select" label="Select action to be performed"> 31 <param name="method_options_selector" type="select" label="Select action to be performed">
29 <option value="percentage" selected="true">Percentage</option> 32 <option value="percentage" selected="true">Percentage</option>
30 <option value="number">Number</option> 33 <option value="number">Number</option>
31 </param> 34 </param>
32 <when value="percentage"> 35 <when value="percentage">
33 <param name="percentage" type="float" value="80.0" label="Pvalue cutoff for binomial distribution test" help="(--percentage)" /> 36 <param name="percentage" type="float" value="80.0" label="Percentage of tags you want to keep" help="Percentage of tags you want to keep. Input 80.0 for 80%.(--percentage)"/>
34 </when> 37 </when>
35 <when value="number"> 38 <when value="number">
36 <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" /> 39 <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" />
37 </when> 40 </when>
38 </conditional> 41 </conditional>
42 <param name="seed" type="integer" value="1" label="Random seed number" min="0" help="Set the random seed while down sampling data. Must be a positive integer in order to be effective. (--seed)"/>
39 </inputs> 43 </inputs>
40 <outputs> 44 <outputs>
41 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" /> 45 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
42 </outputs> 46 </outputs>
43 <tests> 47 <tests>
44 <!-- No test, due to the randomness --> 48 <test>
49 <param name="infile" value="ChIP_200K.bed" ftype="bed" />
50 <param name="method_options_selector" value="percentage" />
51 <param name="percentage" value="80.0" />
52 <param name="seed" value="1" />
53 <output name="outfile" file="bdgrandsample_output.bed"/>
54 </test>
45 </tests> 55 </tests>
46 <help> 56 <help>
57 <![CDATA[
47 **What it does** 58 **What it does**
48 59
49 randsample tool from macs2 60 This is **randsample** utility from the MACS2_ Package. It randomly samples reads by number or percentage from an input file.
61
62 .. _MACS2: https://github.com/taoliu/MACS
50 63
51 @citation@ 64 @citation@
65 ]]>
52 </help> 66 </help>
53 <expand macro="citations" /> 67 <expand macro="citations" />
54 </tool> 68 </tool>