comparison damidseq_core.xml @ 3:e47f77820200 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit a76f114f428e08215ade1bd5cfebd86138243f75

2:69e346fb52a0

<tool id="damidseq_core" name="damidseq" version="0.1.2">
    <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>

    <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 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="--norm_method" type="select" label="Select normalization method">
            <option value="kde">kernel density estimation of log2 GATC fragment ratio (recommended)</option>
            <option value="rpm">readcounts per million reads (not recommended for most use cases)</option>
        </param>
        <param argument="--norm_steps" type="integer" min="1" value="300" label="Number of points in normalisation routine"/>

        <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"/>

3:e47f77820200

<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>

    <configfiles>
        <configfile name="index">A1	Dam
A2	Fusion</configfile>
    </configfiles>
    <inputs>
        <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
        <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam 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 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="--norm_method" type="select" label="Select normalization method">
            <option value="kde">kernel density estimation of log2 GATC fragment ratio (recommended)</option>
            <option value="rpm">readcounts per million reads (not recommended for most use cases)</option>
        </param>
        <param argument="--norm_steps" type="integer" min="1" value="300" label="Number of points in normalisation routine"/>

        <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"/>