Mercurial > repos > jetbrains > span

annotate span.xml @ 11:191a97fe6da5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
https://github.com/JetBrains-Research/galaxy-applications/commit/08f5cc4f954c99934870f39a4ccbeebaf1620634
author jetbrains
date Wed, 16 Jan 2019 12:18:16 -0500
parents 932bcf6c9332
children 6c9ed05526da
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
191a97fe6da5 https://github.com/JetBrains-Research/galaxy-applications/commit/08f5cc4f954c99934870f39a4ccbeebaf1620634
jetbrains
parents: 10
diff changeset
1 <tool id="span" name="SPAN" version="0.9.2.4618">
2
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
2 <description>Semi-supervised Peak Analyzer for ChIP-Seq data</description>
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
3 <requirements>
11
191a97fe6da5 https://github.com/JetBrains-Research/galaxy-applications/commit/08f5cc4f954c99934870f39a4ccbeebaf1620634
jetbrains
parents: 10
diff changeset
4 <requirement type="package" version="0.9.2.4618">package_span_jar</requirement>
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
5 </requirements>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
6 <stdio>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
7 <!-- Wrapper ensures anything other than zero is an error -->
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
8 <exit_code range="1:"/>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
9 <exit_code range=":-1"/>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
10 </stdio>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
11 <command interpreter="python">
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
12 #if str($action.action_selector) == "model"
3
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
13 #if str($control_file) != 'None':
6
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
14 span_wrapper.py
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
15 "${advanced_options.memory}" "${advanced_options.threads}"
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
16 model_with_control
3
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
17 "${genome_file.name}" "${genome_file}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
18 "${treatment_file.name}" "${treatment_file}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
19 "${control_file.name}" "${control_file}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
20 "${bin}"
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
21 #else
6
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
22 span_wrapper.py
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
23 "${advanced_options.memory}" "${advanced_options.threads}"
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
24 model_without_control
3
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
25 "${genome_file.name}" "${genome_file}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
26 "${treatment_file.name}" "${treatment_file}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
27 "${bin}"
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
28 #end if
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
29 #else
3
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
30 #if str($control_file) != 'None':
6
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
31 span_wrapper.py
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
32 "${advanced_options.memory}" "${advanced_options.threads}"
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
33 peaks_with_control
3
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
34 "${genome_file.name}" "${genome_file}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
35 "${treatment_file.name}" "${treatment_file}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
36 "${control_file.name}" "${control_file}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
37 "${bin}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
38 "${action.fdr}" "${action.gap}"
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
39 #else
6
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
40 span_wrapper.py
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
41 "${advanced_options.memory}" "${advanced_options.threads}"
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
42 peaks_without_control
3
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
43 "${genome_file.name}" "${genome_file}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
44 "${treatment_file.name}" "${treatment_file}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
45 "${bin}"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
46 "${action.fdr}" "${action.gap}"
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
47 #end if
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
48 #end if
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
49 </command>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
50 <inputs>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
51 <param name="treatment_file" type="data" format="bam" label="Treatment BAM"
2
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
52 description="Treatment BAM reads to process" argument="--treatment"
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
53 help="Treatment BAM reads to process"/>
3
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
54
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
55 <param name="control_file" type="data" format="BAM" label="Control BAM" optional="True"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
56 argument="--control" help="Control BAM reads to process"/>
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
57
2
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
58 <param name="genome_file" type="data" format="chrom.sizes" label="Genome chrom.sizes"
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
59 description="Genome build chrom.sizes file" argument="--chrom.sizes"
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
60 help="Genome build chrom.sizes file"/>
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
61
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
62 <conditional name="action">
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
63 <param name="action_selector" type="select" label="Action">
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
64 <option value="model">Compute SPAN model</option>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
65 <option value="peaks">Compute SPAN model and produce peaks file</option>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
66 </param>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
67 <when value="peaks">
6
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
68 <param name="fdr" size="5" type="float" value="0.0001" min="0" label="FDR" argument="--fdr"
2
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
69 help="Minimum FDR cutoff to call significant regions, default value is 1.0E-6.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
70 SPAN reports p- and q- values for the null hypothesis that a given bin is not enriched with a histone modification.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
71 Peaks are formed from a list of truly (in the FDR sense) enriched bins for the analyzed biological condition by thresholding the
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
72 Q-value with a cutoff FDR and merging spatially close peaks using GAP option to broad ones. This is equivalent to controlling FDR.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
73 q-values are are calculated from p-values using Benjamini-Hochberg procedure."/>
6
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
74 <param name="gap" size="3" type="integer" value="5" min="0" label="GAP" argument="--gap"
2
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
75 help="Gap size to merge spatially close peaks. Useful for wide histone modifications.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
76 Default value is 5, i.e. peaks separated by 5*BIN distance or less are merged."/>
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
77 </when>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
78 </conditional>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
79
6
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
80 <param name="bin" size="5" type="integer" value="200" min="50" label="Bin size" argument="--bin"
2
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
81 help="Peak analysis is performed on read coverage tiled into consequent bins, with size being configurable.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
82 Default value is 200bp, approximately the length of one nucleosome."/>
6
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
83
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
84 <section name="advanced_options" title="Advanced Options">
9
2a543f239157 Bumped SPAN version to version build 0.9.0.4581 released on Dec 7, 2018
jetbrains
parents: 8
diff changeset
85 <param name="memory" size="6" type="integer" value="4096" min="1024"
2a543f239157 Bumped SPAN version to version build 0.9.0.4581 released on Dec 7, 2018
jetbrains
parents: 8
diff changeset
86 label="Memory limit in megabytes" help="Default value is 4096 megabytes"/>
6
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
87 <param name="threads" argument="--threads" size="2" type="integer" value="2" min="1"
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
88 label="Threads number"
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
89 help="Default value is 2 threads. SPAN utilizes both multithreading and specialized processor extensions like SSE2, AVX, etc."/>
70500fd87b60 Advanced options: threads and memory configuration
jetbrains
parents: 5
diff changeset
90 </section>
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
91 </inputs>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
92 <outputs>
3
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
93 <data name="model.span" format="span" from_work_dir="*.span"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
94 label="SPAN model on ${on_string} (${treatment_file.name}#if str($control_file) != 'None' then '_{}'.format($control_file.name) else '' #_${bin})"/>
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
95 <data name="result.peak" format="bed" from_work_dir="*.peak"
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
96 label="SPAN peaks on ${on_string} (${treatment_file.name}#if str($control_file) != 'None' then '_{}'.format($control_file.name) else '' #_${bin}_${action.fdr}_${action.gap})">
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
97 <filter>action['action_selector'] == "peaks"</filter>
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
98 </data>
3
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
99 <data name="span.log" format="txt" from_work_dir="*.log" label="SPAN logs on ${on_string}"/>
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
100 </outputs>
2
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
101 <help><![CDATA[
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
102 .. class:: infomark
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
103
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
104 **What it does**
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
105
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
106 SPAN Semi-supervised Peak Analyzer is a tool for analyzing ChIP-seq data.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
107
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
108 -----
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
109
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
110 **Inputs**
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
111
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
112 *-t, --treatment <Path>* **Required.** ChIP-seq treatment file. bam, bed or .bed.gz file; If multiple files are given, treated as replicates.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
113
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
114 *--chrom.sizes, --cs <Path>* **Required.** Chromosome sizes path, can be downloaded at http://hgdownload.cse.ucsc.edu/goldenPath/<build>/bigZips/<build>.chrom.sizes
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
115
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
116 *-c, --control <Path>* Control file. bam, bed or bed.gz file; Single control file or separate file per each treatment file required.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
117
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
118 *--fragment <Integer>* Fragment size, read length if not given
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
119
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
120 *-b, --bin <Integer>* Bin size
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
121
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
122 *-f, --fdr <Double>* Fdr value
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
123
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
124 *-g, --gap <Integer>* Gap size to merge peaks
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
125
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
126 *-p, --peaks <Path>* Path to result peaks file in ENCODE broadPeak (BED 6+3) format
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
127
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
128
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
129 -----
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
130
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
131 **Outputs**
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
132
3
4130e95bd6c8 Batch processing mode supported
jetbrains
parents: 2
diff changeset
133 This tool produces a SPAN binary model file (can be visualized in JBR Genome Browser and used in semi-supervised peak calling) and/or peaks in ENCODE broadPeak (BED 6+3) format.
2
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
134
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
135 Peak file columns contain the following data:
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
136
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
137 * **1st**: chromosome name
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
138 * **2nd**: start position of peak
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
139 * **3rd**: end position of peak
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
140 * **4th**: name of peak
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
141 * **5th**: integer score for display in genome browser (e.g. UCSC)
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
142 * **6th**: strand, either "." (=no strand) or "+" or "-"
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
143 * **7th**: fold-change
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
144 * **8th**: -log10pvalue
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
145 * **9th**: -log10qvalue
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
146
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
147 -----
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
148
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
149 **SPAN workflow**
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
150
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
151 * Convert raw reads to tags using *FRAGMENT* parameter.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
152 * Compute coverage for all genome tiled into bins of *BIN* base pairs.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
153 * Fit 3-state hidden Markov model that classifies bins as ZERO states with no coverage, LOW states of non-specific binding, and HIGH states of the specific binding.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
154 * Compute posterior HIGH state probability of each bin.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
155 * Trained model is saved into *.span* binary format.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
156 * Peaks are computed using trained model and *FDR* and *GAP* parameters.
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
157
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
158 ------
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
159
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
160 **Citation**
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
161
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
162 If you use this tool in Galaxy, please cite XXX, et al. *In preparation.*
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
163
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
164 -----
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
165
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
166 **More Information**
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
167
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
168 * Project home page: https://research.jetbrains.org/groups/biolabs/tools/span-peak-analyzer
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
169 * Study cases: https://artyomovlab.wustl.edu/aging
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
170
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
jetbrains
parents: 0
diff changeset
171 ]]></help>
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
jetbrains
parents:
diff changeset
172 </tool>