Mercurial > repos > devteam > sicer

annotate sicer_wrapper.xml @ 3:5c2cc3b58c7d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
author devteam
date Wed, 28 Oct 2020 23:36:25 +0000
parents 74c9214cc8e6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
1 <tool id="peakcalling_sicer" name="SICER" version="@TOOL_VERSION@">
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
2 <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
3 <macros>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
4 <token name="@TOOL_VERSION@">1.1</token>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
5 </macros>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
6 <requirements>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">SICER</requirement>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
8 </requirements>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
10 python '$__tool_directory__/sicer_wrapper.py'
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
11 --bed_file '${input_bed_file}'
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
12 #if str($input_control_file) != 'None':
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
13 --control_file '${input_control_file}'
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
14 --significant_islands_output_file "${significant_islands_output_file}"
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
15 --islands_summary_output_file "${islands_summary_output_file}"
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
16 --significant_islands_summary_output_file "${significant_islands_summary_output_file}"
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
17 #end if
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
18 ${fix_off_by_one_errors}
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
19 --dbkey '${input_bed_file.dbkey}'
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
20 --redundancy_threshold '${redundancy_threshold}'
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
21 --window_size '${window_size}'
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
22 --fragment_size '${fragment_size}'
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
23 --effective_genome_fraction '${effective_genome_fraction}'
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
24 --gap_size '${gap_size}'
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
25 --error_cut_off '${error_cut_off}'
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
26 ##output files
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
27 --stdout "${output_log_file}"
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
28 --redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}"
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
29 --redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}"
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
30 --score_island_output_file "${score_island_output_file}"
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
31 --summary_graph_output_file "${summary_graph_output_file}"
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
32 --test_normalized_wig_output_file "${test_normalized_wig_output_file}"
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
33 --island_filtered_output_file "${island_filtered_output_file}"
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
34 --island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}"
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
35 ]]></command>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
36 <inputs>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
37 <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
38 <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in ['mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8']</validator>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
39 </param>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
40 <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="true"> <!-- fix me, add filter to match dbkeys -->
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
41 <options>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
42 <filter type="data_meta" ref="input_bed_file" key="dbkey" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
43 </options>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
44 </param>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
45 <param name="fix_off_by_one_errors" type="boolean" truevalue="--fix_off_by_one_errors" falsevalue="" checked="true" label="Fix off-by-one errors in output files" help="SICER creates non-standard output files, this option will fix these coordinates"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
46 <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
47 <param name="window_size" type="integer" value="200" label="Window size" help="Resolution of SICER algorithm. For histone modifications, one can use 200 bp" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
48 <param name="fragment_size" type="integer" value="150" label="Fragment size" help="for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75." />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
49 <param name="effective_genome_fraction" type="float" value="0.74" label="Effective genome fraction" help="Effective Genome as fraction of the genome size. It depends on read length." />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
50 <param name="gap_size" type="integer" value="600" label="Gap size" help="Needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ..." />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
51 <param name="error_cut_off" type="float" value="0.01" label="Statistic threshold value" help="FDR (with control) or E-value (without control)" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
52 </inputs>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
53 <outputs>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
54 <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
55 <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)">
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
56 <filter>input_control_file is not None</filter>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
57 </data>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
58 <data name="summary_graph_output_file" format="bedgraph" label="${tool.name} on ${on_string} (test-W${window_size}.graph)"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
59 <data name="test_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (test-W${window_size}-normalized.wig)"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
60 <data name="significant_islands_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-FDR${error_cut_off}-island.bed)">
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
61 <filter>input_control_file is not None</filter>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
62 </data>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
63 <data name="island_filtered_output_file" format="bed" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered.bed' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered.bed' ] ) ) #)"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
64 <data name="island_filtered_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) #)"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
65 <data name="score_island_output_file" format="interval" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '.scoreisland' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '.scoreisland' ] ) ) #)"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
66 <data name="islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary)">
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
67 <filter>input_control_file is not None</filter>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
68 </data>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
69 <data name="significant_islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary-FDR${error_cut_off})">
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
70 <filter>input_control_file is not None</filter>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
71 </data>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
72 <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
73 </outputs>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
74 <tests>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
75 <test>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
76 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
77 <param name="input_control_file" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
78 <param name="fix_off_by_one_errors" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
79 <param name="redundancy_threshold" value="1" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
80 <param name="window_size" value="200" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
81 <param name="fragment_size" value="150" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
82 <param name="effective_genome_fraction" value="0.74" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
83 <param name="gap_size" value="600" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
84 <param name="error_cut_off" value="0.01" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
85 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
86 <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
87 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
88 <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
89 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
90 <output name="score_island_output_file" file="test_1_test-W200-G600-E0.01.scoreisland" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
91 <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
92 </test>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
93 <test>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
94 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
95 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
96 <param name="fix_off_by_one_errors" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
97 <param name="redundancy_threshold" value="1" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
98 <param name="window_size" value="200" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
99 <param name="fragment_size" value="150" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
100 <param name="effective_genome_fraction" value="0.74" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
101 <param name="gap_size" value="600" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
102 <param name="error_cut_off" value="0.01" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
103 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
104 <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
105 <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
106 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
107 <output name="significant_islands_output_file" file="test_2_test-W200-G600-FDR0.01-island.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
108 <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
109 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
110 <output name="score_island_output_file" file="test_2_test-W200-G600.scoreisland" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
111 <output name="islands_summary_output_file" file="test_2_test-W200-G600-islands-summary" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
112 <output name="significant_islands_summary_output_file" file="test_2_test-W200-G600-islands-summary-FDR0.01" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
113 <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
114 </test>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
115 <test>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
116 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
117 <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
118 <param name="fix_off_by_one_errors" value="True" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
119 <param name="redundancy_threshold" value="1" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
120 <param name="window_size" value="200" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
121 <param name="fragment_size" value="150" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
122 <param name="effective_genome_fraction" value="0.74" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
123 <param name="gap_size" value="600" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
124 <param name="error_cut_off" value="0.01" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
125 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
126 <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
127 <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
128 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
129 <output name="significant_islands_output_file" file="test_3_test-W200-G600-FDR0.01-island.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
130 <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
131 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
132 <output name="score_island_output_file" file="test_3_test-W200-G600.scoreisland" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
133 <output name="islands_summary_output_file" file="test_3_test-W200-G600-islands-summary" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
134 <output name="significant_islands_summary_output_file" file="test_3_test-W200-G600-islands-summary-FDR0.01" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
135 <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
136 </test>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
137 <test>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
138 <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
139 <param name="input_control_file" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
140 <param name="fix_off_by_one_errors" value="True" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
141 <param name="redundancy_threshold" value="1" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
142 <param name="window_size" value="200" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
143 <param name="fragment_size" value="150" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
144 <param name="effective_genome_fraction" value="0.74" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
145 <param name="gap_size" value="600" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
146 <param name="error_cut_off" value="0.01" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
147 <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
148 <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
149 <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
150 <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
151 <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
152 <output name="score_island_output_file" file="test_4_test-W200-G600-E0.01.scoreisland" />
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
153 <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
154 </test>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
155 </tests>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
156 <help><![CDATA[
0
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
157 **What it does**
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
158
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
159 SICER first and foremost is a filtering tool. Its main functions are::
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
160
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
161 1. Delineation of the significantly ChIP-enriched regions, which can be used to associate with other genomic landmarks.
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
162 2. Identification of reads on the ChIP-enriched regions, which can be used for profiling and other quantitative analysis.
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
163
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
164 View the original SICER documentation: http://home.gwu.edu/~wpeng/Software.htm.
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
165
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
166 ------
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
167
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
168 .. class:: warningmark
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
169
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
170 By default, SICER creates files that do not conform to standards (e.g. BED files are closed, not half-open). This could have implications for downstream analysis.
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
171 To force the output of SICER to be formatted properly to standard file formats, check the **"Fix off-by-one errors in output files"** option.
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
172
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
173 ------
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
174
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
175 **Citation**
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
176 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
3
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
177 ]]></help>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
178 <citations>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
179 <citation type="doi">10.1093/bioinformatics/btp340</citation>
5c2cc3b58c7d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"
devteam
parents: 2
diff changeset
180 </citations>
0
82a8234e03f2 Imported from capsule None
devteam
parents:
diff changeset
181 </tool>