span: span.xml annotate

annotate span.xml @ 9:2a543f239157 draft

Bumped SPAN version to version build 0.9.0.4581 released on Dec 7, 2018 https://github.com/JetBrains-Research/galaxy-applications/commit/e9e440d6fe82bba5cdb92262d423eed6c0f72845

author	jetbrains
date	Wed, 12 Dec 2018 04:11:14 -0500
parents	66b2c9a128ab
children	932bcf6c9332

rev	line source
9 2a543f239157 Bumped SPAN version to version build 0.9.0.4581 released on Dec 7, 2018 jetbrains parents: 8 diff changeset	1 <tool id="span" name="SPAN" version="0.9.0.4581">
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>
9 2a543f239157 Bumped SPAN version to version build 0.9.0.4581 released on Dec 7, 2018 jetbrains parents: 8 diff changeset	4 <requirement type="package" version="0.9.0.4581">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>

Mercurial > repos > jetbrains > span

annotate span.xml @ 9:2a543f239157 draft