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comparison span.xml @ 6:70500fd87b60 draft

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Advanced options: threads and memory configuration
author jetbrains
date Wed, 21 Nov 2018 10:31:58 -0500
parents d87ecbc477d8
children caaea0a5c425
comparison
equal deleted inserted replaced
5:d87ecbc477d8 6:70500fd87b60
1 <tool id="span" name="SPAN" version="0.7.1.4518"> 1 <tool id="span" name="SPAN" version="0.7.1.4518a">
2 <description>Semi-supervised Peak Analyzer for ChIP-Seq data</description> 2 <description>Semi-supervised Peak Analyzer for ChIP-Seq data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.7.1.4518">package_span_jar</requirement> 4 <requirement type="package" version="0.7.1.4518">package_span_jar</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
9 <exit_code range=":-1"/> 9 <exit_code range=":-1"/>
10 </stdio> 10 </stdio>
11 <command interpreter="python"> 11 <command interpreter="python">
12 #if str($action.action_selector) == "model" 12 #if str($action.action_selector) == "model"
13 #if str($control_file) != 'None': 13 #if str($control_file) != 'None':
14 span_wrapper.py model_with_control 14 span_wrapper.py
15 "${advanced_options.memory}" "${advanced_options.threads}"
16 model_with_control
15 "${genome_file.name}" "${genome_file}" 17 "${genome_file.name}" "${genome_file}"
16 "${treatment_file.name}" "${treatment_file}" 18 "${treatment_file.name}" "${treatment_file}"
17 "${control_file.name}" "${control_file}" 19 "${control_file.name}" "${control_file}"
18 "${bin}" 20 "${bin}"
19 #else 21 #else
20 span_wrapper.py model_without_control 22 span_wrapper.py
23 "${advanced_options.memory}" "${advanced_options.threads}"
24 model_without_control
21 "${genome_file.name}" "${genome_file}" 25 "${genome_file.name}" "${genome_file}"
22 "${treatment_file.name}" "${treatment_file}" 26 "${treatment_file.name}" "${treatment_file}"
23 "${bin}" 27 "${bin}"
24 #end if 28 #end if
25 #else 29 #else
26 #if str($control_file) != 'None': 30 #if str($control_file) != 'None':
27 span_wrapper.py peaks_with_control 31 span_wrapper.py
32 "${advanced_options.memory}" "${advanced_options.threads}"
33 peaks_with_control
28 "${genome_file.name}" "${genome_file}" 34 "${genome_file.name}" "${genome_file}"
29 "${treatment_file.name}" "${treatment_file}" 35 "${treatment_file.name}" "${treatment_file}"
30 "${control_file.name}" "${control_file}" 36 "${control_file.name}" "${control_file}"
31 "${bin}" 37 "${bin}"
32 "${action.fdr}" "${action.gap}" 38 "${action.fdr}" "${action.gap}"
33 #else 39 #else
34 span_wrapper.py peaks_without_control 40 span_wrapper.py
41 "${advanced_options.memory}" "${advanced_options.threads}"
42 peaks_without_control
35 "${genome_file.name}" "${genome_file}" 43 "${genome_file.name}" "${genome_file}"
36 "${treatment_file.name}" "${treatment_file}" 44 "${treatment_file.name}" "${treatment_file}"
37 "${bin}" 45 "${bin}"
38 "${action.fdr}" "${action.gap}" 46 "${action.fdr}" "${action.gap}"
39 #end if 47 #end if
55 <param name="action_selector" type="select" label="Action"> 63 <param name="action_selector" type="select" label="Action">
56 <option value="model">Compute SPAN model</option> 64 <option value="model">Compute SPAN model</option>
57 <option value="peaks">Compute SPAN model and produce peaks file</option> 65 <option value="peaks">Compute SPAN model and produce peaks file</option>
58 </param> 66 </param>
59 <when value="peaks"> 67 <when value="peaks">
60 <param name="fdr" size="5" type="float" value="0.0001" label="FDR" argument="--fdr" 68 <param name="fdr" size="5" type="float" value="0.0001" min="0" label="FDR" argument="--fdr"
61 help="Minimum FDR cutoff to call significant regions, default value is 1.0E-6. 69 help="Minimum FDR cutoff to call significant regions, default value is 1.0E-6.
62 SPAN reports p- and q- values for the null hypothesis that a given bin is not enriched with a histone modification. 70 SPAN reports p- and q- values for the null hypothesis that a given bin is not enriched with a histone modification.
63 Peaks are formed from a list of truly (in the FDR sense) enriched bins for the analyzed biological condition by thresholding the 71 Peaks are formed from a list of truly (in the FDR sense) enriched bins for the analyzed biological condition by thresholding the
64 Q-value with a cutoff FDR and merging spatially close peaks using GAP option to broad ones. This is equivalent to controlling FDR. 72 Q-value with a cutoff FDR and merging spatially close peaks using GAP option to broad ones. This is equivalent to controlling FDR.
65 q-values are are calculated from p-values using Benjamini-Hochberg procedure."/> 73 q-values are are calculated from p-values using Benjamini-Hochberg procedure."/>
66 <param name="gap" size="5" type="integer" value="5" label="GAP" argument="--gap" 74 <param name="gap" size="3" type="integer" value="5" min="0" label="GAP" argument="--gap"
67 help="Gap size to merge spatially close peaks. Useful for wide histone modifications. 75 help="Gap size to merge spatially close peaks. Useful for wide histone modifications.
68 Default value is 5, i.e. peaks separated by 5*BIN distance or less are merged."/> 76 Default value is 5, i.e. peaks separated by 5*BIN distance or less are merged."/>
69 </when> 77 </when>
70 </conditional> 78 </conditional>
71 79
72 <param name="bin" size="5" type="integer" value="200" label="Bin size" argument="--bin" 80 <param name="bin" size="5" type="integer" value="200" min="50" label="Bin size" argument="--bin"
73 help="Peak analysis is performed on read coverage tiled into consequent bins, with size being configurable. 81 help="Peak analysis is performed on read coverage tiled into consequent bins, with size being configurable.
74 Default value is 200bp, approximately the length of one nucleosome."/> 82 Default value is 200bp, approximately the length of one nucleosome."/>
83
84 <section name="advanced_options" title="Advanced Options">
85 <param name="memory" size="6" type="integer" value="2048" min="1024"
86 label="Memory limit in megabytes" help="Default value is 2048 megabytes"/>
87 <param name="threads" argument="--threads" size="2" type="integer" value="2" min="1"
88 label="Threads number"
89 help="Default value is 2 threads. SPAN utilizes both multithreading and specialized processor extensions like SSE2, AVX, etc."/>
90 </section>
75 </inputs> 91 </inputs>
76 <outputs> 92 <outputs>
77 <data name="model.span" format="span" from_work_dir="*.span" 93 <data name="model.span" format="span" from_work_dir="*.span"
78 label="SPAN model on ${on_string} (${treatment_file.name}#if str($control_file) != 'None' then '_{}'.format($control_file.name) else '' #_${bin})"/> 94 label="SPAN model on ${on_string} (${treatment_file.name}#if str($control_file) != 'None' then '_{}'.format($control_file.name) else '' #_${bin})"/>
79 <data name="result.peak" format="bed" from_work_dir="*.peak" 95 <data name="result.peak" format="bed" from_work_dir="*.peak"