comparison span.xml @ 6:70500fd87b60 draft

Advanced options: threads and memory configuration

5:d87ecbc477d8

<tool id="span" name="SPAN" version="0.7.1.4518">
    <description>Semi-supervised Peak Analyzer for ChIP-Seq data</description>
    <requirements>
        <requirement type="package" version="0.7.1.4518">package_span_jar</requirement>
    </requirements>
    <stdio>

        <exit_code range=":-1"/>
    </stdio>
    <command interpreter="python">
#if str($action.action_selector) == "model"
    #if str($control_file) != 'None':
        span_wrapper.py model_with_control
            "${genome_file.name}" "${genome_file}"
            "${treatment_file.name}" "${treatment_file}"
            "${control_file.name}" "${control_file}"
            "${bin}"
    #else
        span_wrapper.py model_without_control
            "${genome_file.name}" "${genome_file}"
            "${treatment_file.name}" "${treatment_file}"
            "${bin}"
    #end if
#else
    #if str($control_file) != 'None':
        span_wrapper.py peaks_with_control
            "${genome_file.name}" "${genome_file}"
            "${treatment_file.name}" "${treatment_file}"
            "${control_file.name}" "${control_file}"
            "${bin}"
            "${action.fdr}" "${action.gap}"
    #else
        span_wrapper.py peaks_without_control
            "${genome_file.name}" "${genome_file}"
            "${treatment_file.name}" "${treatment_file}"
            "${bin}"
            "${action.fdr}" "${action.gap}"
    #end if

            <param name="action_selector" type="select" label="Action">
                <option value="model">Compute SPAN model</option>
                <option value="peaks">Compute SPAN model and produce peaks file</option>
            </param>
            <when value="peaks">
                <param name="fdr" size="5" type="float" value="0.0001" label="FDR" argument="--fdr"
                       help="Minimum FDR cutoff to call significant regions, default value is 1.0E-6.
                       SPAN reports p- and q- values for the null hypothesis that a given bin is not enriched with a histone modification.
                       Peaks are formed from a list of truly (in the FDR sense) enriched bins for the analyzed biological condition by thresholding the
                       Q-value with a cutoff FDR and merging spatially close peaks using GAP option to broad ones. This is equivalent to controlling FDR.
                       q-values are are calculated from p-values using Benjamini-Hochberg procedure."/>
                <param name="gap" size="5" type="integer" value="5" label="GAP" argument="--gap"
                       help="Gap size to merge spatially close peaks. Useful for wide histone modifications.
                       Default value is 5, i.e. peaks separated by 5*BIN distance or less are merged."/>
            </when>
        </conditional>

        <param name="bin" size="5" type="integer" value="200" label="Bin size" argument="--bin"
               help="Peak analysis is performed on read coverage tiled into consequent bins, with size being configurable.
               Default value is 200bp, approximately the length of one nucleosome."/>
    </inputs>
    <outputs>
        <data name="model.span" format="span" from_work_dir="*.span"
              label="SPAN model on ${on_string} (${treatment_file.name}#if str($control_file) != 'None' then '_{}'.format($control_file.name) else '' #_${bin})"/>
        <data name="result.peak" format="bed" from_work_dir="*.peak"

6:70500fd87b60

<tool id="span" name="SPAN" version="0.7.1.4518a">
    <description>Semi-supervised Peak Analyzer for ChIP-Seq data</description>
    <requirements>
        <requirement type="package" version="0.7.1.4518">package_span_jar</requirement>
    </requirements>
    <stdio>

        <exit_code range=":-1"/>
    </stdio>
    <command interpreter="python">
#if str($action.action_selector) == "model"
    #if str($control_file) != 'None':
        span_wrapper.py
            "${advanced_options.memory}" "${advanced_options.threads}"
            model_with_control
            "${genome_file.name}" "${genome_file}"
            "${treatment_file.name}" "${treatment_file}"
            "${control_file.name}" "${control_file}"
            "${bin}"
    #else
        span_wrapper.py
            "${advanced_options.memory}" "${advanced_options.threads}"
            model_without_control
            "${genome_file.name}" "${genome_file}"
            "${treatment_file.name}" "${treatment_file}"
            "${bin}"
    #end if
#else
    #if str($control_file) != 'None':
        span_wrapper.py
            "${advanced_options.memory}" "${advanced_options.threads}"
            peaks_with_control
            "${genome_file.name}" "${genome_file}"
            "${treatment_file.name}" "${treatment_file}"
            "${control_file.name}" "${control_file}"
            "${bin}"
            "${action.fdr}" "${action.gap}"
    #else
        span_wrapper.py
            "${advanced_options.memory}" "${advanced_options.threads}"
            peaks_without_control
            "${genome_file.name}" "${genome_file}"
            "${treatment_file.name}" "${treatment_file}"
            "${bin}"
            "${action.fdr}" "${action.gap}"
    #end if

            <param name="action_selector" type="select" label="Action">
                <option value="model">Compute SPAN model</option>
                <option value="peaks">Compute SPAN model and produce peaks file</option>
            </param>
            <when value="peaks">
                <param name="fdr" size="5" type="float" value="0.0001" min="0" label="FDR" argument="--fdr"
                       help="Minimum FDR cutoff to call significant regions, default value is 1.0E-6.
                       SPAN reports p- and q- values for the null hypothesis that a given bin is not enriched with a histone modification.
                       Peaks are formed from a list of truly (in the FDR sense) enriched bins for the analyzed biological condition by thresholding the
                       Q-value with a cutoff FDR and merging spatially close peaks using GAP option to broad ones. This is equivalent to controlling FDR.
                       q-values are are calculated from p-values using Benjamini-Hochberg procedure."/>
                <param name="gap" size="3" type="integer" value="5" min="0" label="GAP" argument="--gap"
                       help="Gap size to merge spatially close peaks. Useful for wide histone modifications.
                       Default value is 5, i.e. peaks separated by 5*BIN distance or less are merged."/>
            </when>
        </conditional>

        <param name="bin" size="5" type="integer" value="200" min="50" label="Bin size" argument="--bin"
               help="Peak analysis is performed on read coverage tiled into consequent bins, with size being configurable.
               Default value is 200bp, approximately the length of one nucleosome."/>

        <section name="advanced_options" title="Advanced Options">
            <param name="memory" size="6" type="integer" value="2048" min="1024"
                   label="Memory limit in megabytes" help="Default value is 2048 megabytes"/>
            <param name="threads" argument="--threads" size="2" type="integer" value="2" min="1"
                   label="Threads number"
                   help="Default value is 2 threads. SPAN utilizes both multithreading and specialized processor extensions like SSE2, AVX, etc."/>
        </section>
    </inputs>
    <outputs>
        <data name="model.span" format="span" from_work_dir="*.span"
              label="SPAN model on ${on_string} (${treatment_file.name}#if str($control_file) != 'None' then '_{}'.format($control_file.name) else '' #_${bin})"/>
        <data name="result.peak" format="bed" from_work_dir="*.peak"