comparison damidseq_core.xml @ 6:9b13b8bda9d8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 8dccd750ac2057caa6495636153250bdd4ecf549

5:6c00620084a5

<tool id="damidseq_core" name="damidseq" version="0.1.3">
    <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>

        --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>

        <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>
            <option value="full">Full</option>
        </param>
        <param argument="--full_data_files" type="boolean" truevalue="--full_data_file" falsevalue="" label="Output full binned ratio files (not only GATC array)"/>
        <param argument="--len" type="integer" min="50" value="300" label="Length to extend reads to"/>
        <param argument="--bins" type="integer" min="10" value="75" label="Width of bins to use for mapping reads"/>
        <param argument="--min_norm_value" type="float" value="-5.0" label="Minimum log2 value to limit normalisation search at"/>
        <param argument="--max_norm_value" type="float" value="5.0" label="Maximum log2 value to limit normalisation search at"/>
        <param argument="--method_subtract" type="boolean" truevalue="--method_subtract" falsevalue="" label="Subtract Dam control values from Dam-fusion values instead of using the log2 ratio?"/>

        <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="0.9" 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">

                        <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"/>

            <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[

6:9b13b8bda9d8

<tool id="damidseq_core" name="damidseq" version="0.1.4">
    <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>

        --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.gatc.* gatc.output
        #if str($full_data_files):
            && mv Fusion-vs-Dam.* full.output
        #end if
    ]]></command>
    <configfiles>
        <configfile name="index">A1	Dam
A2	Fusion</configfile>
    </configfiles>

        <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>
            <option value="full">Full</option>
        </param>
        <param argument="--full_data_files" type="boolean" truevalue="--full_data_files" falsevalue="" label="Output full binned ratio files (not only GATC array)"/>
        <param argument="--len" type="integer" min="50" value="300" label="Length to extend reads to"/>
        <param argument="--bins" type="integer" min="10" value="75" label="Width of bins to use for mapping reads"/>
        <param argument="--min_norm_value" type="float" value="-5.0" label="Minimum log2 value to limit normalisation search at"/>
        <param argument="--max_norm_value" type="float" value="5.0" label="Maximum log2 value to limit normalisation search at"/>
        <param argument="--method_subtract" type="boolean" truevalue="--method_subtract" falsevalue="" label="Subtract Dam control values from Dam-fusion values instead of using the log2 ratio?"/>

        <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="0.9" max="1.0" label="max decile for normalising from fusion-protein array"/>
    </inputs>
    <outputs>
        <data name="output_ratio" format="bedgraph" from_work_dir="gatc.output" label="Dam-fusion vs Dam-only GATC ratio on ${on_string}">
            <change_format>
                <when input="output_format" value="gff" format="gff" />
            </change_format>
            <actions>
                <action type="metadata" name="dbkey">

                        <filter type="param_value" ref="reference_index" column="0"/>
                    </option>
                </action>
            </actions>
        </data>
        <data name="output_ratio_full" format="bedgraph" from_work_dir="full.output" label="Dam-fusion vs Dam-only full ratio on ${on_string}">
            <filter>full_data_files == '--full_data_files'</filter>
            <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 on ${on_string}">
            <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 on ${on_string}">
            <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"/>

            <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"/>
            <param name="full_data_files" value="true"/>
            <output name="output_ratio" file="output_ratio.bed"/>
            <output name="output_ratio_full" file="output_ratio_full.bed"/>
            <output name="control_output" file="control.bam"/>
            <output name="fusion_output" file="fusion.bam"/>
        </test>
    </tests>
    <help><![CDATA[