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Initial version of SPAN for ToolShed
author jetbrains
date Thu, 15 Nov 2018 11:04:49 -0500
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children 5b99943c4627
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-1:000000000000 0:1f0c4f0a9c3b
1 <tool id="span" name="SPAN" version="0.7.1.4272">
2 <description>ChIP-Seq analysis</description>
3 <requirements>
4 <requirement type="package" version="0.7.1.4272">package_span_jar</requirement>
5 <!--<container type="docker">biolabs/span</container>-->
6 </requirements>
7 <stdio>
8 <!-- Wrapper ensures anything other than zero is an error -->
9 <exit_code range="1:"/>
10 <exit_code range=":-1"/>
11 </stdio>
12 <command interpreter="python">
13 #if str($action.action_selector) == "model"
14 #if $control.control_selector
15 span_wrapper.py model with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}"
16 #else
17 span_wrapper.py model without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}"
18 #end if
19 #else
20 #if $control.control_selector
21 span_wrapper.py peaks with_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${control.control_file}" "${fdr}" "${gap}" "${action.peaks_file}"
22 #else
23 span_wrapper.py peaks without_control "${genome}" "${treatment_file}" "${bin}" "${action.model_file}" "${fdr}" "${gap}" "${action.peaks_file}"
24 #end if
25 #end if
26 </command>
27 <inputs>
28 <param name="treatment_file" type="data" format="bam" label="Treatment BAM"
29 description="Treatment BAM reads to process"/>
30 <param name="genome" type="data" format="chrom.sizes" label="Genome chrom.sizes"
31 description="Genome build chrom.sizes file"/>
32
33 <conditional name="control">
34 <param name="control_selector" type="boolean" label="Control available" value="false"/>
35 <when value="true">
36 <param name="control_file" type="data" format="bam" label="Control BAM"
37 description="Control BAM reads to process"/>
38 </when>
39 </conditional>
40
41 <conditional name="action">
42 <param name="action_selector" type="select" label="Action">
43 <option value="model">Compute SPAN model</option>
44 <option value="peaks">Compute SPAN model and produce peaks file</option>
45 </param>
46 <when value="model">
47 <param name="model_file" type="text" value="model.span" label="Model name"/>
48 </when>
49 <when value="peaks">
50 <param name="model_file" type="text" value="model.span" label="Model file name"/>
51 <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
52 <param name="gap" size="5" type="integer" value="5" label="GAP"/>
53 <param name="peaks_file" type="text" value="result.peak" label="Peaks file name"/>
54 </when>
55 </conditional>
56
57 <param name="bin" size="5" type="integer" value="200" label="Bin size"/>
58 </inputs>
59 <outputs>
60 <data name="${action.model_file}" format="span" label="SPAN model file"/>
61 <data name="${action.peaks_file}" format="bed" label="SPAN peaks file">
62 <filter>action['action_selector'] == "peaks"</filter>
63 </data>
64 </outputs>
65 <help>
66 SPAN Semi-supervised Peak Analyzer is a tool for analyzing ChIP-seq data.
67 Details: http://artyomovlab.wustl.edu/aging/span.html
68 </help>
69 </tool>