comparison control_freec.xml @ 1:1204e79d3a99 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

0:5330cf818142

<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>

        #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
            ln -s '$reference_source.ref.fields.path' ./genome.fa &&
            ln -s '${reference_source.ref.fields.path}.fai' ./genome.fa.fai &&
        #end if

        #if int($WGS_WES.advanced_settings.window_section.window) == 0
            ln -s '$WGS_WES.input_capture_file' ./capture.bed &&
        #end if

        mkdir ./chromosomes &&
        mkdir ./output &&

        #if $output_section.makeGraph
            && R -f `which makeGraph.R` '$WGS_WES.advanced_settings.ploidy' 'output/sample.bam_ratio.txt'
        #end if

        #if $output_section.circos_data
            && python '$__tool_directory__/ratio2circos.py'
               -i ./output/sample.bam_ratio.BedGraph
               -p '$WGS_WES.advanced_settings.ploidy'
               -o sample.bam_ratio_log2_circos.txt
        #end if
    ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[
#import os

            <filter>output_section['makeGraph']</filter>
        </data>
        <data name="out_gc_profile" format="tabular" label="${tool.name} on ${on_string}: GC-content profile" from_work_dir="output/GC_profile.targetedRegions.cnp">
            <filter>int(WGS_WES['advanced_settings']['window_section']['window']) == 0</filter>
        </data>
        <data name="out_ratio_log2_circos" format="tabular" label="${tool.name} on ${on_string}: Circos 2D-track data" from_work_dir="output/sample.bam_ratio_log2_circos.txt">
            <filter>output_section['circos_data']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="5">

1:1204e79d3a99

<tool id="control_freec" name="Control-FREEC" version="@WRAPPER_VERSION@">
    <description>detects copy-number changes and allelic imbalances</description>
    <xrefs>
        <xref type="bio.tools">freec</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="5.0.1">gawk</requirement>

        #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
            ln -s '$reference_source.ref.fields.path' ./genome.fa &&
            cp '${reference_source.ref.fields.path}.fai' ./genome.fa.fai &&
        #end if

        #if int($WGS_WES.advanced_settings.window_section.window) == 0
            ln -s '$WGS_WES.input_capture_file' ./capture.bed &&

            cat ./capture.bed | cut -f 1 | sort | uniq > ./capture.bed_tmp &&
            cp ./genome.fa.fai ./genome.fa.fai_tmp &&
            awk 'NR==FNR{A[$1];next}($1 in A)' ./capture.bed_tmp ./genome.fa.fai_tmp > ./genome.fa.fai &&
        #end if

        mkdir ./chromosomes &&
        mkdir ./output &&

        #if $output_section.makeGraph
            && R -f `which makeGraph.R` '$WGS_WES.advanced_settings.ploidy' 'output/sample.bam_ratio.txt'
        #end if

        #if $output_section.circos_data
            && python '$__tool_directory__/ratio2circos.py' '$WGS_WES.advanced_settings.ploidy'
        #end if
    ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[
#import os

            <filter>output_section['makeGraph']</filter>
        </data>
        <data name="out_gc_profile" format="tabular" label="${tool.name} on ${on_string}: GC-content profile" from_work_dir="output/GC_profile.targetedRegions.cnp">
            <filter>int(WGS_WES['advanced_settings']['window_section']['window']) == 0</filter>
        </data>
        <data name="out_ratio_log2_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Log2 Ratio (2D Data Track)" from_work_dir="output/sample.bam_ratio_log2_circos.txt">
            <filter>output_section['circos_data']</filter>
        </data>
        <data name="out_chr_sorted_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Karyotype" from_work_dir="output/karyotype_circos.txt">
            <filter>output_section['circos_data']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="5">