comparison tag_pileup_frequency.xml @ 3:580e8bcb6413 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency commit 92a9933fda38241c033dad1f709a928f66756b6f"

2:6432735cdb22

<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.1">
    <description></description>
    <requirements>
        <requirement type="package" version="8.0.112">openjdk</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
mkdir -p output &&
ln -f -s '${input1.metadata.bam_index}' '${input1}.bai' &&
java -jar '$__tool_directory__/TagPileup.jar'
-b '$input1'
-i '${input1}.bai'
-c '$input2'
-s $tag_shift
-n $bin_size
-e $tags_equal
-r $reads
-p $proper_pe

        <param name="input2" type="data" format="bed" label="Bed file" />
        <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" />
        <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" />
        <param  name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" />
        <param  name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input">
            <option value="0" selected="True">Read1</option>
            <option value="1">Read2</option>
            <option value="2">combined</option>
        </param>
        <param  name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/>
        <param  name="combine_strands" type="select" label="Combine strands?">
            <option value="0" selected="True">No</option>
            <option value="1">Yes</option>
        </param>
        <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" />
        <param name="output_heatmap" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output frequencies heatmap?" />
    </inputs>

            <param name="reads" value="0" />
            <param name="proper_pe" value="false" />
            <param name="combine_strands" value="0" />
            <param name="composite_smoothing_window" value="0" />
            <param name="output_heatmap" value="true" />
            <output name="output1" file="output1.tabular" ftype="tabular"/>
            <output_collection name="heatmaps" type="list">
                <element name="dataset_2_dataset_1_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/>
                <element name="dataset_2_dataset_1_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/>
            </output_collection>
        </test>
    </tests>
    <help>

3:580e8bcb6413

<tool id="tag_pileup_frequency" name="Tag pileup frequency" version="1.0.2">
    <description></description>
    <requirements>
        <requirement type="package" version="11.0.1">openjdk</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#import re
#set input1_identifier = re.sub('[^\s\w\-]', '_', str($input1.element_identifier))
#set input2_identifier = re.sub('[^\s\w\-]', '_', str($input2.element_identifier))
mkdir -p output &&
ln -s '${input1}' '${input1_identifier}' &&
ln -s '${input2}' '${input2_identifier}' &&
ln -s '${input1.metadata.bam_index}' '${input1_identifier}.bai' &&
java -jar '$__tool_directory__/TagPileup.jar'
-b '${input1_identifier}'
-i '${input1_identifier}.bai'
-c '$input2_identifier'
-s $tag_shift
-n $bin_size
-e $tags_equal
-r $reads
-p $proper_pe

        <param name="input2" type="data" format="bed" label="Bed file" />
        <param name="tag_shift" type="integer" value="0" min="0" label="5' to 3' Tag Shift (bp)" />
        <param name="bin_size" type="integer" value="1" min="1" label="Bin Size (bp)" />
        <param  name="tags_equal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set Tags to be equal?" />
        <param  name="reads" type="select" label="Reads to examine" help="Selecting combined requires paired-end BAM input">
            <option value="0" selected="true">Read1</option>
            <option value="1">Read2</option>
            <option value="2">combined</option>
        </param>
        <param  name="proper_pe" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require proper PE?" help="Requires paired-end BAM input"/>
        <param  name="combine_strands" type="select" label="Combine strands?">
            <option value="0" selected="true">No</option>
            <option value="1">Yes</option>
        </param>
        <param name="composite_smoothing_window" type="integer" value="0" min="0" label="Composite smoothing window (bp)" />
        <param name="output_heatmap" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Output frequencies heatmap?" />
    </inputs>

            <param name="reads" value="0" />
            <param name="proper_pe" value="false" />
            <param name="combine_strands" value="0" />
            <param name="composite_smoothing_window" value="0" />
            <param name="output_heatmap" value="true" />
            <output name="output1" file="output1.tabular" ftype="tabular" compare="contains"/>
            <output_collection name="heatmaps" type="list">
                <element name="input_bed_input_bam_read1_anti.tabular" file="input2_input1_read1_anti.tabular" ftype="tabular" compare="contains"/>
                <element name="input_bed_input_bam_read1_sense.tabular" file="input2_input1_read1_sense.tabular" ftype="tabular" compare="contains"/>
            </output_collection>
        </test>
    </tests>
    <help>