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annotate span.xml @ 2:5b99943c4627 draft

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Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a
author jetbrains
date Sun, 18 Nov 2018 08:20:27 -0500
parents 1f0c4f0a9c3b
children 4130e95bd6c8
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1 <tool id="span" name="SPAN" version="0.7.1.4272">
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2 <description>Semi-supervised Peak Analyzer for ChIP-Seq data</description>
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3 <requirements>
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4 <requirement type="package" version="0.7.1.4272">package_span_jar</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Wrapper ensures anything other than zero is an error -->
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8 <exit_code range="1:"/>
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9 <exit_code range=":-1"/>
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10 </stdio>
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11 <command interpreter="python">
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12 #import re
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13 #set treatment_identifier = re.sub('[^\w\-\.]', '_', str($treatment_file.element_identifier))
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14 #set genome_identifier = re.sub('[^\w\-\.]', '_', str($genome_file.element_identifier))
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16 #if $control.control_selector
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17 #set control_identifier = re.sub('[^\w\-\.]', '_', str($control.control_file.element_identifier))
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18 #end if
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19
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20 #if str($action.action_selector) == "model"
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21 #if $control.control_selector
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22 span_wrapper.py model with_control
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23 "${genome_identifier}" "${genome_file}"
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24 "${treatment_identifier}" "${treatment_file}"
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25 "${bin}" "${action.model_file}"
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26 "${control_identifier}" "${control.control_file}"
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27 #else
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28 span_wrapper.py model without_control
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29 "${genome_identifier}" "${genome_file}"
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30 "${treatment_identifier}" "${treatment_file}"
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31 "${bin}" "${action.model_file}"
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32 #end if
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33 #else
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34 #if $control.control_selector
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35 span_wrapper.py peaks with_control
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36 "${genome_identifier}" "${genome_file}"
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37 "${treatment_identifier}" "${treatment_file}"
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38 "${bin}" "${action.model_file}"
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39 "${control_identifier}" "${control.control_file}"
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40 "${action.fdr}" "${action.gap}" "${action.peaks_file}"
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41 #else
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42 span_wrapper.py peaks without_control
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43 "${genome_identifier}" "${genome_file}"
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44 "${treatment_identifier}" "${treatment_file}"
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45 "${bin}" "${action.model_file}"
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46 "${action.fdr}" "${action.gap}" "${action.peaks_file}"
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47 #end if
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48 #end if
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49 </command>
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50 <inputs>
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51 <param name="treatment_file" type="data" format="bam" label="Treatment BAM"
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52 description="Treatment BAM reads to process" argument="--treatment"
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53 help="Treatment BAM reads to process"/>
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54 <param name="genome_file" type="data" format="chrom.sizes" label="Genome chrom.sizes"
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55 description="Genome build chrom.sizes file" argument="--chrom.sizes"
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56 help="Genome build chrom.sizes file"/>
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57
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58 <conditional name="control">
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59 <param name="control_selector" type="boolean" label="Control available" value="false"/>
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60 <when value="true">
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61 <param name="control_file" type="data" format="bam" label="Control BAM"
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62 description="Control BAM reads to process" argument="--control"
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63 help="Control BAM reads to process"/>
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64 </when>
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65 </conditional>
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66
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67 <conditional name="action">
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68 <param name="action_selector" type="select" label="Action">
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69 <option value="model">Compute SPAN model</option>
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70 <option value="peaks">Compute SPAN model and produce peaks file</option>
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71 </param>
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72 <when value="model">
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73 <param name="model_file" type="text" value="model.span" label="Model name"
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74 help="Trained model file in binary format, which can be visualized directly in JBR Genome Browser
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75 and used in integrated peak calling pipeline"/>
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76 </when>
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77 <when value="peaks">
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78 <param name="model_file" type="text" value="model.span" label="Model file name"
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79 help="Trained model file in binary format, which can be visualized directly in JBR Genome Browser
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80 and used in integrated peak calling pipeline"/>
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81 <param name="fdr" size="5" type="float" value="0.0001" label="FDR" argument="--fdr"
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82 help="Minimum FDR cutoff to call significant regions, default value is 1.0E-6.
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83 SPAN reports p- and q- values for the null hypothesis that a given bin is not enriched with a histone modification.
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84 Peaks are formed from a list of truly (in the FDR sense) enriched bins for the analyzed biological condition by thresholding the
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85 Q-value with a cutoff FDR and merging spatially close peaks using GAP option to broad ones. This is equivalent to controlling FDR.
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86 q-values are are calculated from p-values using Benjamini-Hochberg procedure."/>
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87 <param name="gap" size="5" type="integer" value="5" label="GAP" argument="--gap"
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88 help="Gap size to merge spatially close peaks. Useful for wide histone modifications.
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89 Default value is 5, i.e. peaks separated by 5*BIN distance or less are merged."/>
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90 <param name="peaks_file" type="text" value="result.peak" label="Peaks file name" argument="--peaks"/>
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91 </when>
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92 </conditional>
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93
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94 <param name="bin" size="5" type="integer" value="200" label="Bin size" argument="--bin"
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95 help="Peak analysis is performed on read coverage tiled into consequent bins, with size being configurable.
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96 Default value is 200bp, approximately the length of one nucleosome."/>
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97 </inputs>
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98 <outputs>
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99 <data name="SPAN model file" format="span" from_work_dir="*.span" label="SPAN model file ${action.model_file} on ${on_string}"/>
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100 <data name="SPAN peaks file" format="bed" from_work_dir="*.peak" label="SPAN peaks file ${action.peaks_file} on ${on_string}">
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101 <filter>action['action_selector'] == "peaks"</filter>
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102 </data>
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103 <data name="SPAN log file" format="txt" from_work_dir="*.log" label="SPAN log file on ${on_string}"/>
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104 </outputs>
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105 <help><![CDATA[
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106 .. class:: infomark
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107
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108 **What it does**
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109
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110 SPAN Semi-supervised Peak Analyzer is a tool for analyzing ChIP-seq data.
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111
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112 -----
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114 **Inputs**
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116 *-t, --treatment <Path>* **Required.** ChIP-seq treatment file. bam, bed or .bed.gz file; If multiple files are given, treated as replicates.
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118 *--chrom.sizes, --cs <Path>* **Required.** Chromosome sizes path, can be downloaded at http://hgdownload.cse.ucsc.edu/goldenPath/<build>/bigZips/<build>.chrom.sizes
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120 *-c, --control <Path>* Control file. bam, bed or bed.gz file; Single control file or separate file per each treatment file required.
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122 *--fragment <Integer>* Fragment size, read length if not given
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124 *-b, --bin <Integer>* Bin size
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126 *-f, --fdr <Double>* Fdr value
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128 *-g, --gap <Integer>* Gap size to merge peaks
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130 *-p, --peaks <Path>* Path to result peaks file in ENCODE broadPeak (BED 6+3) format
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133 -----
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135 **Outputs**
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137 This tool produces a SPAN binary model file and/or peaks in ENCODE broadPeak (BED 6+3) format.
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139 Peak file columns contain the following data:
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140
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141 * **1st**: chromosome name
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142 * **2nd**: start position of peak
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143 * **3rd**: end position of peak
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144 * **4th**: name of peak
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145 * **5th**: integer score for display in genome browser (e.g. UCSC)
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146 * **6th**: strand, either "." (=no strand) or "+" or "-"
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147 * **7th**: fold-change
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148 * **8th**: -log10pvalue
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149 * **9th**: -log10qvalue
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151 -----
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153 **SPAN workflow**
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155 * Convert raw reads to tags using *FRAGMENT* parameter.
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156 * Compute coverage for all genome tiled into bins of *BIN* base pairs.
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157 * 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.
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158 * Compute posterior HIGH state probability of each bin.
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159 * Trained model is saved into *.span* binary format.
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160 * Peaks are computed using trained model and *FDR* and *GAP* parameters.
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162 ------
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164 **Citation**
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166 If you use this tool in Galaxy, please cite XXX, et al. *In preparation.*
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168 -----
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170 **More Information**
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172 * Project home page: https://research.jetbrains.org/groups/biolabs/tools/span-peak-analyzer
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173 * Study cases: https://artyomovlab.wustl.edu/aging
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175 ]]></help>
0
1f0c4f0a9c3b Initial version of SPAN for ToolShed
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176 </tool>