comparison damidseq_core.xml @ 1:0d1514ecd757 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e

0:eb3a145c4962

<tool id="damidseq_core" name="damidseq" version="0.1.0">
    <description>align, extend and normalize a DAMID-seq experiment</description>
    <requirements>
        <requirement type="package" version="1.4">damidseq_pipeline</requirement>
    </requirements>
    <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
        export HOME="\$PWD" &&
        ln -f -s '$dam' A001.$dam.ext &&
        ln -f -s '$dam_fusion' A002.$dam_fusion.ext &&
        ln -f -s '$index' index.txt &&
        damidseq_pipeline
        --bins=$bins
        --bowtie=1
        --bowtie2_genome_dir='$reference_index.fields.path'
        --extend_reads=$extend_reads
        --extension_method='$extension_method'

        --output_format=$output_format
        --q=$q
        --qscore1max=$qscore1max
        --qscore1min=$qscore1min
        --qscore2max=$qscore2max
        --threads=\${GALAXY_SLOTS:-4} &&
        mv Fusion-vs-Dam.*.$output_format fusion.output
    ]]></command>
    <configfiles>
        <configfile name="index">A1	Dam
A2	Fusion</configfile>
    </configfiles>
    <inputs>
        <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control DAM alignment file"/>
        <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="DAM fusion alignment file"/>
        <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
          <options from_data_table="bowtie2_indexes">
            <filter type="sort_by" column="2"/>
            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
          </options>
        </param>
        <param argument="--gatc_frag_file" type="data" format="gff" label="GFF file with all GATC locations"/>
        <param name="output_format" type="select" label="Select the output format for the peaks">
            <option value="bedgraph">Bedgraph</option>
            <option value="gff">GFF</option>
        </param>
        <param argument="--extend_reads" type="boolean" truevalue="1" falsevalue="0" checked="True" label="Perform read extension?"/>
        <param argument="--extension_method" type="select" label="Select the read extension method" help="Select Full to extend all reads or GATC to extend reads to --len or to the next GATC site, whichever is shorter. Using this option increases peak resolution (default).">
            <option value="gatc">To nearest GATC site</option>

        <param argument="--qscore1min" type="float" min="0.0" value="0.4" max="1.0" label="min decile for normalising from Dam array"/>
        <param argument="--qscore1max" type="float" min="0.0" value="1.0" max="1.0" label="max decile for normalising from Dam array"/>
        <param argument="--qscore2max" type="float" min="0.0" value="1.0" max="1.0" label="max decile for normalising from fusion-protein array"/>
    </inputs>
    <outputs>
        <data name="output_ratio" format="bedgraph" from_work_dir="fusion.output" label="DAM-fusion vs Dam-only ratio">
            <change_format>
                <when input="output_format" value="gff" format="gff" />
            </change_format>
        </data>
        <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="DAM-only alignment"/>
        <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="DAM-fusion alignment"/>
    </outputs>
    <tests>
        <test>
            <param name="dam" value="A001.fastq"/>
            <param name="dam_fusion" value="A002.fastq"/>
            <param name="gatc_frag_file" value="dm6.GATC.gff"/>
            <param name="index" value="dm6"/>
            <param name="norm_method" value="rpm"/>
            <output name="output_ratio" file="output_ratio.bedgraph"/>
            <output name="control_output" file="control.bam"/>
            <output name="fusion_output" file="fusion.bam"/>
        </test>
    </tests>
    <help><![CDATA[

1:0d1514ecd757

<tool id="damidseq_core" name="damidseq" version="0.1.1">
    <description>align, extend and normalize a DamID-seq experiment</description>
    <requirements>
        <requirement type="package" version="1.4">damidseq_pipeline</requirement>
    </requirements>
    <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
        ln -f -s '$dam' A001.fastq &&
        ln -f -s '$dam_fusion' A002.fastq &&
        ln -f -s '$index' index.txt &&
        HOME="\$PWD" damidseq_pipeline
        --bins=$bins
        --bowtie=1
        --bowtie2_genome_dir='$reference_index.fields.path'
        --extend_reads=$extend_reads
        --extension_method='$extension_method'

        --output_format=$output_format
        --q=$q
        --qscore1max=$qscore1max
        --qscore1min=$qscore1min
        --qscore2max=$qscore2max
        --threads=\${GALAXY_SLOTS:-4} 2>&1| LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' &&
        mv Fusion-vs-Dam.* fusion.output
    ]]></command>
    <configfiles>
        <configfile name="index">A1	Dam
A2	Fusion</configfile>
    </configfiles>
    <inputs>
        <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
        <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="DAM fusion fastq"/>
        <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
          <options from_data_table="bowtie2_indexes">
            <filter type="sort_by" column="2"/>
            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
          </options>
        </param>
        <param argument="--gatc_frag_file" type="data" format="gff" label="GFF file with all GATC locations"/>
        <param name="output_format" type="select" label="Select the output format for the peaks">
            <option value="bedgraph">Bed</option>
            <option value="gff">GFF</option>
        </param>
        <param argument="--extend_reads" type="boolean" truevalue="1" falsevalue="0" checked="True" label="Perform read extension?"/>
        <param argument="--extension_method" type="select" label="Select the read extension method" help="Select Full to extend all reads or GATC to extend reads to --len or to the next GATC site, whichever is shorter. Using this option increases peak resolution (default).">
            <option value="gatc">To nearest GATC site</option>

        <param argument="--qscore1min" type="float" min="0.0" value="0.4" max="1.0" label="min decile for normalising from Dam array"/>
        <param argument="--qscore1max" type="float" min="0.0" value="1.0" max="1.0" label="max decile for normalising from Dam array"/>
        <param argument="--qscore2max" type="float" min="0.0" value="1.0" max="1.0" label="max decile for normalising from fusion-protein array"/>
    </inputs>
    <outputs>
        <data name="output_ratio" format="bed" from_work_dir="fusion.output" label="DAM-fusion vs Dam-only ratio">
            <change_format>
                <when input="output_format" value="gff" format="gff" />
            </change_format>
            <actions>
                <action type="metadata" name="dbkey">
                    <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
                        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                        <filter type="param_value" ref="reference_index" column="0"/>
                    </option>
                </action>
            </actions>
        </data>
        <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="DAM-only alignment">
            <actions>
                <action type="metadata" name="dbkey">
                    <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
                        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                        <filter type="param_value" ref="reference_index" column="0"/>
                    </option>
                </action>
            </actions>
        </data>
        <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="DAM-fusion alignment">
            <actions>
                <action type="metadata" name="dbkey">
                    <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
                        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                        <filter type="param_value" ref="reference_index" column="0"/>
                    </option>
                </action>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="dam" value="A001.fastq"/>
            <param name="dam_fusion" value="A002.fastq"/>
            <param name="gatc_frag_file" value="dm6.GATC.gff"/>
            <param name="reference_index" value="dm6"/>
            <param name="norm_method" value="rpm"/>
            <output name="output_ratio" file="output_ratio.bed"/>
            <output name="control_output" file="control.bam"/>
            <output name="fusion_output" file="fusion.bam"/>
        </test>
    </tests>
    <help><![CDATA[