comparison control_freec.xml @ 2:f923c54a17ee draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"

1:2c6349fb175c

<tool id="control_freec" name="Control-FREEC" version="@WRAPPER_VERSION@">
    <description>detects copy-number changes and allelic imbalances</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="5.0.1">gawk</requirement>
        <requirement type="package" version="@TOOL_VERSION@">control-freec</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($reference_source.ref_selector) == 'history':
            ln -s '$reference_source.ref' ./genome.fa &&
            samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for control-freec' >&2 &&
        #else

        mkdir ./output &&

        awk -F " " '/^>/ {close(F); F="chromosomes/"substr($1,2)".fa"} {print >> F}' ./genome.fa &&

        ln -s '$WGS_WES.input_sample_file' ./sample.bam &&
        #if $input_control_file
            ln -s '$WGS_WES.input_control_file' ./control.bam &&
        #end if

        freec
            -conf '$script_file'

mateFile = sample.bam
inputFormat = BAM
mateOrientation = $WGS_WES.mateOrientation_selector

[control]
mateFile = control.bam
inputFormat = BAM
mateOrientation = $WGS_WES.mateOrientation_selector

#if int($WGS_WES.advanced_settings.window_section.window) == 0
[target]
captureRegions = capture.bed
#end if

                <option value="WGS" selected="True">whole-genome sequencing (WGS)</option>
                <option value="WES">whole-exome sequencing (WES)</option>
                <option value="other">other method</option>
            </param>
            <when value="WGS">
                <expand macro="def_input_files" />
                <section name="advanced_settings" title="Advanced WGS settings" expanded="false">
                    <expand macro="WGS" />
                    <expand macro="shared" />
                </section>
            </when>

        <expand macro="reference_interface" />
        <expand macro="output_section" />
    </inputs>
    <outputs>
        <data name="out_sample_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (sample)" from_work_dir="output/sample.bam_sample.cpn" />
        <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn" />
        <data name="out_sample_coord" format="tabular" label="${tool.name} on ${on_string}: Coordinates of predicted CN alterations" from_work_dir="output/sample.bam_CNVs" />
        <data name="out_sample_info" format="txt" label="${tool.name} on ${on_string}: Information about FREEC run" from_work_dir="output/sample.bam_info.txt" />
        <data name="out_sample_ratio" format="tabular" label="${tool.name} on ${on_string}: Ratios and predicted CN alterations for each window" from_work_dir="output/sample.bam_ratio.txt" />
        <data name="out_sample_subclones" format="txt" label="${tool.name} on ${on_string}: Subclones" from_work_dir="output/sample.bam_subclones.txt" >
            <filter>int(WGS_WES['advanced_settings']['minimalSubclonePresence']) != 100</filter>

                    <has_text text="Chromosome"/>
                </assert_contents>
            </output>
            <output name="out_gc_profile" file="output/GC_profile.targetedRegions.cnp" />
        </test>
    </tests>
    <help><![CDATA[
Control-FREEC
=============

2:f923c54a17ee

<tool id="control_freec" name="Control-FREEC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>detects copy-number changes and allelic imbalances</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        #if str($reference_source.ref_selector) == 'history':
            ln -s '$reference_source.ref' ./genome.fa &&
            samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for control-freec' >&2 &&
        #else

        mkdir ./output &&

        awk -F " " '/^>/ {close(F); F="chromosomes/"substr($1,2)".fa"} {print >> F}' ./genome.fa &&

        ln -s '$WGS_WES.input_sample_file' ./sample.bam &&
        #if $WGS_WES.input_control_file
            ln -s '$WGS_WES.input_control_file' ./control.bam &&
        #end if

        freec
            -conf '$script_file'

mateFile = sample.bam
inputFormat = BAM
mateOrientation = $WGS_WES.mateOrientation_selector

[control]
#if $WGS_WES.input_control_file
mateFile = control.bam
inputFormat = BAM
mateOrientation = $WGS_WES.mateOrientation_selector
#end if

#if int($WGS_WES.advanced_settings.window_section.window) == 0
[target]
captureRegions = capture.bed
#end if

                <option value="WGS" selected="True">whole-genome sequencing (WGS)</option>
                <option value="WES">whole-exome sequencing (WES)</option>
                <option value="other">other method</option>
            </param>
            <when value="WGS">
                <expand macro="wgs_input_files" />
                <section name="advanced_settings" title="Advanced WGS settings" expanded="false">
                    <expand macro="WGS" />
                    <expand macro="shared" />
                </section>
            </when>

        <expand macro="reference_interface" />
        <expand macro="output_section" />
    </inputs>
    <outputs>
        <data name="out_sample_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (sample)" from_work_dir="output/sample.bam_sample.cpn" />
        <data name="out_control_raw" format="tabular" label="${tool.name} on ${on_string}: Raw copy number profiles (control)" from_work_dir="output/control.bam_control.cpn">
            <filter>WGS_WES['input_control_file']</filter>
        </data>
        <data name="out_sample_coord" format="tabular" label="${tool.name} on ${on_string}: Coordinates of predicted CN alterations" from_work_dir="output/sample.bam_CNVs" />
        <data name="out_sample_info" format="txt" label="${tool.name} on ${on_string}: Information about FREEC run" from_work_dir="output/sample.bam_info.txt" />
        <data name="out_sample_ratio" format="tabular" label="${tool.name} on ${on_string}: Ratios and predicted CN alterations for each window" from_work_dir="output/sample.bam_ratio.txt" />
        <data name="out_sample_subclones" format="txt" label="${tool.name} on ${on_string}: Subclones" from_work_dir="output/sample.bam_subclones.txt" >
            <filter>int(WGS_WES['advanced_settings']['minimalSubclonePresence']) != 100</filter>

                    <has_text text="Chromosome"/>
                </assert_contents>
            </output>
            <output name="out_gc_profile" file="output/GC_profile.targetedRegions.cnp" />
        </test>
        <!-- Test without control file-->
        <test expect_num_outputs="4">
            <conditional name="reference_source">
                <param name="ref_selector" value="history"/>
                <param name="ref" ftype="fasta" value="genome.fasta" />
            </conditional>
            <param name="WGS_WES_selector" value="WGS" />
            <param name="input_sample_file" ftype="bam" value="tumor.bam" />
            <param name="mateOrientation_selector" value="0" />
            <param name="minimalSubclonePresence" value="100" />
            <param name="window" value="50" />
            <param name="step" value="10" />
            <output name="out_sample_raw" file="output/sample.bam_sample_woc.cpn" />
            <output name="out_sample_coord" file="output/sample_woc.bam_CNVs" />
            <output name="out_sample_info" file="output/sample.bam_info_woc.txt" />
            <output name="out_sample_ratio" file="output/sample.bam_ratio_woc.txt" />
        </test>
    </tests>
    <help><![CDATA[
Control-FREEC
=============