comparison repenrich.xml @ 4:d1f7ab78f7b5 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f

3:1c9810ba0638

<tool id="repenrich" name="RepEnrich" version="1.4.3">
    <description>Repeat Element Profiling</description>
    <requirements>
        <requirement type="package" version="1.2.0">bowtie</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="2.20.1">bedtools</requirement>

    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set input_base = 'Sample'
        #set baseReference = 'Genome'
        ln -f -s '$genome' '${baseReference}.fa' &&
        ln -f -s '$input_fastq' '${input_base}.fastq' &&
        #if $seq_method.seq_method_list == "paired-end":
            ln -f -s '$input2_fastq' '${input_base}_2.fastq' &&
        #end if
        bowtie-build '$genome' ${baseReference} &&
        python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} &&
        #if $seq_method.seq_method_list == "single-read":
            bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
            TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&

            <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/>
            <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/>
            <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/>
            <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/>
        </test>
  </tests>

    <help>

**What it does**

4:d1f7ab78f7b5

<tool id="repenrich" name="RepEnrich" version="1.5.0">
    <description>Repeat Element Profiling</description>
    <requirements>
        <requirement type="package" version="1.2.0">bowtie</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="2.20.1">bedtools</requirement>

    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set input_base = 'Sample'
        #set baseReference = 'Genome'

        ## uncompress fastq.gz or fastqsanger.gz if needed
        #if $seq_method.seq_method_list == "single-read":
            #if $input_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
                gunzip < '$input_fastq' > '${input_base}.fastq' &&
            #else:
                ln -f -s '$input_fastq' '${input_base}.fastq' &&
            #end if
        #else:
            #if $input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
                gunzip < '$input_fastq' > '${input_base}.fastq' &&
                gunzip < '$input2_fastq' > '${input_base}_2.fastq' &&                
            #else:
                ln -f -s '$input_fastq' '${input_base}.fastq' &&
                ln -f -s '$input2_fastq' '${input_base}_2.fastq' &&
            #end if
        #end if
        
        ln -f -s '$genome' '${baseReference}.fa' &&
        bowtie-build '$genome' ${baseReference} &&
        python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} &&
        #if $seq_method.seq_method_list == "single-read":
            bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
            TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&

            <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/>
            <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/>
            <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/>
            <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/>
        </test>
        <test>
            <param name="seq_method_list" value="single-read"/>
            <param name="input_fastq" value="Samp.fastq.gz" ftype="fastq.gz"/>
            <param name="genome" value="chrM.fa" ftype="fasta"/>
            <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
            <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/>
            <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/>
            <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/>
            <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/>
        </test>
         <test>
            <param name="seq_method_list" value="paired-end"/>
            <param name="input_fastq" value="Samp_L.fastq.gz" ftype="fastq.gz"/>
            <param name="input2_fastq" value="Samp_R.fastq.gz" ftype="fastq.gz"/>
            <param name="genome" value="chrM.fa" ftype="fasta"/>
            <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
            <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/>
            <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/>
            <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/>
            <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/>
        </test>
  </tests>

    <help>

**What it does**