comparison manta.xml @ 4:d09254e37c68 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"

3:d648e40c6da9

                  --scanSizeMb=${advanced.scanSizeMb}
                  --callMemMb=${advanced.callMemMb} &&

    ln -s -f '${run_dir}/runWorkflow.py' '${run_manta_workflow}' &&
    ln -s -f './configManta.py.ini' '${set_conf_file}' &&
    python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4} &&
    cp '${run_dir}/results/variants/candidateSV.vcf.gz' '${out_vcf1}' &&
    cp '${run_dir}/results/variants/diploidSV.vcf.gz' '${out_vcf2}' &&
    cp '${run_dir}/results/variants/candidateSmallIndels.vcf.gz' '${out_vcf3}'

    ]]></command>

    <inputs>
        <expand macro="reference_source_conditional" />

                <param name="normal_bam_file" type="data" format="bam" label="select normal BAM" help="Select the files you wish to send to Manta (normal sample, it must be in BAM format)." />
                <param name="tumor_bam_file" type="data" format="bam" label="select tumor BAM" help="Select the files you wish to send to Manta (tumor sample, it must be in BAM format)." />
            </when>
        </conditional>

        <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional outputs" help="Additional parameters.">
            <option value="exome">Set options for WES input: turn off depth filters</option>
            <option value="rna">Set options for RNA-Seq input. Must specify exactly one bam input file</option>
            <option value="unstrandedRNA">Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand</option>
        </param>

        <section name="advanced" title="Advanced options" expanded="false">

            <param name="callMemMb" type="integer" value="8000" label="Set default task memory requirements" help="The maximum memory size to assign to tasks" />
            <param name="scanSizeMb" type="integer" value="12" label="Set maximum sequence region size" help="The maximum sequence region size (in megabases) scanned by each task during SV Locus graph generation. (default: 12)" />
            <param name="retainTempFiles" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Keep all temporary files" help="Click yes so all temporary files (for workflow debugging) will be kept."/>
            <param name="generateEvidenceBam" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Generate a bam of supporting reads for all SVs" help="Click yes for generating a BAM of supporting reads for all SVs."/>

        </section>

        <!-- <expand macro="manta_configuration"/> -->

        <conditional name="set_configuration">
            <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?">
                <option value="Default_config_file">Default</option>    
                <option value="Custom_config_file">Upload a different config file</option>
                <option value="Customized">Customize the options</option>
            </param>
            <when value="Default_config_file">
            </when>
            <when value="Custom_config_file">
                <param format="ini" name="CustomConfigFile" type="data" label="config file"/>

            </when>
        </conditional>

        <param name="runworkflow_file_check" type="boolean" label="output manta run_workflow file" checked="False" help="Show run_workflow file on history"/>
        <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/>
        <param name="O1_check" type="boolean" label="snvs filtred" checked="False" help="Show filtred snvs"/>
        <param name="O2_check" type="boolean" label="indels filtred" checked="False" help="Show filtred indels"/>
        <param name="O3_check" type="boolean" label="all snvs" checked="False" help="Show snvs"/>
        
    </inputs>

    <outputs>

        <data format="txt" name="run_manta_workflow" label="Parameters for running Manta">
            <filter>runworkflow_file_check == True</filter>
        </data>

        <data format="tabular" name="set_conf_file" label="conf_file.ini">
            <filter>config_file_check == True</filter>
        </data>
        <data format="vcf_bgzip" name="out_vcf1" label="${tool.name} on ${on_string} (Generating the candidateSV.vcf file)" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz">
            <filter>O1_check == True</filter>
        </data>
        <data format="vcf_bgzip" name="out_vcf2" label="${tool.name} on ${on_string} (Generating the diploidSV.vcf file)" from_work_dir="MantaWorkflow/results/variants/diploidSV.vcf.gz">
            <filter>O2_check == True</filter>
        </data>
        <data format="vcf_bgzip" name="out_vcf3" label="${tool.name} on ${on_string} (Generating the candidateSmallIndels.vcf file)" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz">
            <filter>O3_check == True</filter>
        </data>
    </outputs>

    <tests>
                <test>
                        <conditional name="reference_source">
                                <param name="reference_source_selector" value="cached"/>
                                <param name="index" value="hg19"/>
                        </conditional>

                        <conditional name="bam_input">
                                <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
                                <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
                                <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
                        </conditional>

                        <conditional name="set_configuration">
                                <param name="set_configuration_switch" value="Default_config_file"/>
                        </conditional>
                        <param name="callMemMb" value="1000"/>
                        <param name="O3_check" value="True"/>
                        <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
                </test>
                <test>
                        <conditional name="reference_source">
                                <param name="reference_source_selector" value="history"/>
                                <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
                        </conditional>

                        <conditional name="bam_input">
                                <param name="bam_input_selector" value="tumor_bam"/>
                                <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
                                <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
                        </conditional>

                        <conditional name="set_configuration">
                                <param name="set_configuration_switch" value="Default_config_file"/>
                        </conditional>
                        <param name="callMemMb" value="1000"/>
                        <param name="O1_check" value="True"/>
                        <output name="out_vcf1" file="candidateSV.vcf.gz" decompress="true" lines_diff="4"/>
                </test>
                <test>
                        <conditional name="reference_source">
                                <param name="reference_source_selector" value="history"/>
                                <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
                        </conditional>

                        <conditional name="bam_input">
                                <param name="bam_input_selector" value="tumor_bam"/>
                                <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
                                <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
                        </conditional>

                        <conditional name="set_configuration">
                                <param name="set_configuration_switch" value="Default_config_file"/>
                        </conditional>
                        <param name="callMemMb" value="1000"/>
                        <param name="O3_check" value="True"/>
                        <output name="out_vcf3" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
                </test>
        </tests>
        
    <help><![CDATA[
**Manta**
This script configures the Manta SV analysis pipeline.
You must specify a BAM or CRAM file for at least one sample.
Configuration will produce a workflow run script which
can execute the workflow on a single node or through
sge and resume any interrupted execution.

**Options**
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  --config=FILE         provide a configuration file to override defaults in

**Extended options**
    These options are either unlikely to be reset after initial site
    configuration or only of interest for workflow development/debugging.
    They will not be printed here if a default exists unless --allHelp is
    specified
    --existingAlignStatsFile=FILE
                        Pre-calculated alignment statistics file. Skips
                        alignment stats calculation.
    --useExistingChromDepths
                        Use pre-calculated chromosome depths.

4:d09254e37c68

                  --scanSizeMb=${advanced.scanSizeMb}
                  --callMemMb=${advanced.callMemMb} &&

    ln -s -f '${run_dir}/runWorkflow.py' '${run_manta_workflow}' &&
    ln -s -f './configManta.py.ini' '${set_conf_file}' &&
    python2 '${run_dir}/runWorkflow.py' -m local -j \${GALAXY_SLOTS:-4}

    ]]></command>

    <inputs>
        <expand macro="reference_source_conditional" />

                <param name="normal_bam_file" type="data" format="bam" label="select normal BAM" help="Select the files you wish to send to Manta (normal sample, it must be in BAM format)." />
                <param name="tumor_bam_file" type="data" format="bam" label="select tumor BAM" help="Select the files you wish to send to Manta (tumor sample, it must be in BAM format)." />
            </when>
        </conditional>

        <param name="additional_param" type="select" multiple="true" display="checkboxes" label="Additional parameters" >
            <option value="exome">Set options for WES input: turn off depth filters</option>
            <option value="rna">Set options for RNA-Seq input. Must specify exactly one bam input file</option>
            <option value="unstrandedRNA">Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand</option>
        </param>

        <section name="advanced" title="Advanced options" expanded="false">

            <param name="callMemMb" type="integer" value="8000" label="Set default task memory requirements" help="The maximum memory size to assign to tasks" />
            <param name="scanSizeMb" type="integer" value="12" label="Set maximum sequence region size" help="The maximum sequence region size (in megabases) scanned by each task during SV Locus graph generation. (default: 12)" />
            <!-- <param name="generateEvidenceBam" type="boolean" checked="False" truevalue="-s" falsevalue="" label="Generate a bam of supporting reads for all SVs" help="Click yes for generating a BAM of supporting reads for all SVs."/> -->

        </section>

        <!-- <expand macro="manta_configuration"/> -->

        <conditional name="set_configuration">
            <param name="set_configuration_switch" type="select" label="Do you want to change default configuration settings?">
                <option value="Default_config_file">Default Manta Configuration File</option>    
                <option value="Custom_config_file">Upload your Own Configuration File</option>
                <option value="Customized">Customize a Configuration File using this Galaxy Form</option>
            </param>
            <when value="Default_config_file">
            </when>
            <when value="Custom_config_file">
                <param format="ini" name="CustomConfigFile" type="data" label="config file"/>

            </when>
        </conditional>

        <param name="runworkflow_file_check" type="boolean" label="output manta run_workflow file" checked="False" help="Show run_workflow file on history"/>
        <param name="config_file_check" type="boolean" label="output conf file" checked="False" help="Show configuration file on history"/>
        <param name="candidateSV_check" type="boolean" label="Unscored candidate SV and indels" checked="False"
               help="Show unfiltered structural variants"/>
        <param name="candidateSmallIndels_check" type="boolean" label="all snvs" checked="False"
               help="Subset of the Unscored candidate SV and indels, containing only simple insertion and deletion variants"/>
        <param name="diploidSV_check" type="boolean" label="filtered variants in diploid model" checked="False"
               help="Show filtered variants in a diploid (only normal) model. In the case of a tumor/normal subtraction, the scores in this file *do not*
                     reflect any information from the tumor sample" />
        <param name="somaticSV_check" type="boolean" label="SVs and indels scored under a somatic variant model" checked="False"
               help="This file will only be produced if a tumor sample alignment file is supplied during configuration"/>
    </inputs>

    <outputs>
        <data format="txt" name="run_manta_workflow" label="Parameters for running Manta">
            <filter>runworkflow_file_check == True</filter>
        </data>

        <data format="tabular" name="set_conf_file" label="conf_file.ini">
            <filter>config_file_check == True</filter>
        </data>
        <data format="vcf_bgzip" name="candidateSV" label="Manta unfiltered SVs" from_work_dir="MantaWorkflow/results/variants/candidateSV.vcf.gz">
            <filter>candidateSV_check == True</filter>
        </data>
        <data format="vcf_bgzip" name="candidateSmallIndels" label="Manta unfiltered Small Indels" from_work_dir="MantaWorkflow/results/variants/candidateSmallIndels.vcf.gz">
            <filter>candidateSmallIndels_check == True</filter>
        </data>
        <data format="vcf_bgzip" name="diploidSV" label="Manta SVs (diploid model)" from_work_dir="MantaWorkflow/results/variants/diploidSV.vcf.gz">
            <filter>diploidSV_check == True</filter>
        </data>
        <data format="vcf_bgzip" name="somaticSV" label="Manta SVs (somatic model)" from_work_dir="MantaWorkflow/results/variants/somaticSV.vcf.gz">
            <filter>somaticSV_check == True</filter>
        </data>
    </outputs>

    <tests>
        <test>
                <param name="reference_source_selector" value="cached"/>
                <param name="index" value="hg19"/>
                <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
                <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
                <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
                <param name="set_configuration_switch" value="Default_config_file"/>
                <param name="callMemMb" value="1000"/>
                <param name="candidateSmallIndels_check" value="True"/>
                <param name="somaticSV_check" value="True"/>
                <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
                <output name="somaticSV" file="somaticSV.vcf.gz" decompress="true" lines_diff="4"/>
        </test>
        <test>
                <param name="reference_source_selector" value="cached"/>
                <param name="index" value="hg19"/>
                <param name="bam_input_selector" value="tumor_bam" dbkey="hg19"/>
                <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
                <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
                <param name="set_configuration_switch" value="Default_config_file"/>
                <param name="callMemMb" value="1000"/>
                <param name="candidateSmallIndels_check" value="True"/>
                <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
        </test>
        <test>
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
                <param name="bam_input_selector" value="tumor_bam"/>
                <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
                <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
                <param name="set_configuration_switch" value="Default_config_file"/>
                <param name="callMemMb" value="1000"/>
                <param name="candidateSV_check" value="True"/>
                <output name="candidateSV" file="candidateSV.vcf.gz" decompress="true" lines_diff="4"/>
        </test>
        <test>
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" ftype="fasta" value="hg19_region.fa"/>
                <param name="bam_input_selector" value="tumor_bam"/>
                <param name="normal_bam_file" ftype="bam" value="HCC1954_normal.bam"/>
                <param name="tumor_bam_file" ftype="bam" value="HCC1954_tumor.bam"/>
                <param name="set_configuration_switch" value="Default_config_file"/>
                <param name="callMemMb" value="1000"/>
                <param name="candidateSmallIndels_check" value="True"/>
                <output name="candidateSmallIndels" file="candidateSmallIndels.vcf.gz" decompress="true" lines_diff="4"/>
        </test>
 </tests>

    <help><![CDATA[
**Outputs**
  The primary Manta outputs are a set of VCF 4.1 files. Currently there are 3 VCF files
  created for a germline analysis, and an additional somatic VCF is produced for a
  tumor/normal subtraction. These files are:
  
  - diploidSV.vcf.gz
      SVs and indels scored and genotyped under a diploid model for the set of samples in a
      joint diploid sample analysis or for the normal sample in a tumor/normal subtraction
      analysis. **In the case of a tumor/normal subtraction, the scores in this file do not
      reflect any information from the tumor sample.**
  
  - somaticSV.vcf.gz
      SVs and indels scored under a somatic variant model. This file will only be produced
      if a tumor sample alignment file is supplied during configuration
  
  - candidateSV.vcf.gz
      Unscored SV and indel candidates. Only a minimal amount of supporting evidence is
      required for an SV to be entered as a candidate in this file. An SV or indel must be a
      candidate to be considered for scoring, therefore an SV cannot appear in the other VCF
      outputs if it is not present in this file. Note that by default this file includes
      indels of size 8 and larger. The smallest indels in this set are intended to be passed
      on to a small variant caller without scoring by manta itself (by default manta scoring
      starts at size 50).
  
  - candidateSmallIndels.vcf.gz
      Subset of the candidateSV.vcf.gz file containing only simple insertion and deletion
      variants less than the minimum scored variant size (50 by default). Passing this file
      to a small variant caller will provide continuous coverage over all indel sizes when
      the small variant caller and manta outputs are evaluated together. Alternate small
      indel candidate sets can be parsed out of the candidateSV.vcf.gz file if this
      candidate set is not appropriate.
  
  For tumor-only analysis, Manta will produce an additional VCF:

  - tumorSV.vcf.gz
      Subset of the candidateSV.vcf.gz file after removing redundant candidates and small
      indels less than the minimum scored variant size (50 by default). The SVs are not
      scored, but include additional details: (1) paired and split read supporting evidence
      counts for each allele (2) a subset of the filters from the scored tumor-normal model
      are applied to the single tumor case to improve precision.

**Manta helps**
  This script configures the Manta SV analysis pipeline.
  You must specify a BAM or CRAM file for at least one sample.
  Configuration will produce a workflow run script which
  can execute the workflow on a single node or through
  sge and resume any interrupted execution.

**Options**
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  --config=FILE         provide a configuration file to override defaults in

**Extended options**
    These options are either unlikely to be reset after initial site
    configuration or only of interest for workflow development/debugging.
    They will not be printed here if a default exists unless --allHelp is
    specified
    
    --existingAlignStatsFile=FILE
                        Pre-calculated alignment statistics file. Skips
                        alignment stats calculation.
    --useExistingChromDepths
                        Use pre-calculated chromosome depths.