comparison qualimap_multi_bamqc.xml @ 3:17b35d23731f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b

2:e38af83df163

<tool id="qualimap_multi_bamqc" name="QualiMap Multi-Sample BamQC" version="@VERSION@">
    <macros>
        <import>qualimap_macros.xml</import>
        <xml name="test_collection">
            <collection type="list">
                <element name="genome_results" value="genome_results_inside_features.txt" />

                <element name="mapping_quality_across_reference" value="mapping_quality_across_reference.txt" />
                <element name="mapping_quality_histogram" value="mapping_quality_histogram.txt" />
            </collection>
        </xml>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        #if str($input.mode) == 'grouped':
          #set $n = 0

                <option value="grouped">In groups</option>
            </param>
            <when value="individual">
                <repeat name="bam_qc_data" default="2" min="2"
                title="BAM QC data to combine">
                    <param name="bam_qc_input" type="data_collection" collection_type="list" format="txt"
                    label="Single-sample BAM QC data"
                    help="" />
                    <param name="sample_name" type="text"
                    label="Name to use for this dataset"
                    help="This is the name that will be used for this dataset throughout the Qualimap report. Default: Name of the raw data collection in the history" />
                </repeat>
            </when>

                    <param name="name" type="text" label="Name of the group">
                        <validator type="expression" message="A name is required for every group">value.strip()</validator>
                    </param>
                    <repeat name="bam_qc_data" default="1" min="1"
                    title="Data associated with this group">
                        <param name="bam_qc_input" type="data_collection" collection_type="list" format="txt" multiple="true"
                        label="Single-sample BAM QC data"
                        help="" />
                    </repeat>
                </repeat>
            </when>
        </conditional>
    </inputs>

3:17b35d23731f

<tool id="qualimap_multi_bamqc" name="QualiMap Multi-Sample BamQC" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <macros>
        <import>qualimap_macros.xml</import>
        <xml name="test_collection">
            <collection type="list">
                <element name="genome_results" value="genome_results_inside_features.txt" />

                <element name="mapping_quality_across_reference" value="mapping_quality_across_reference.txt" />
                <element name="mapping_quality_histogram" value="mapping_quality_histogram.txt" />
            </collection>
        </xml>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        #if str($input.mode) == 'grouped':
          #set $n = 0

                <option value="grouped">In groups</option>
            </param>
            <when value="individual">
                <repeat name="bam_qc_data" default="2" min="2"
                title="BAM QC data to combine">
                    <param name="bam_qc_input" type="data_collection" format="txt" label="Single-sample BAM QC data" help="" collection_type="list" />
                    <param name="sample_name" type="text"
                    label="Name to use for this dataset"
                    help="This is the name that will be used for this dataset throughout the Qualimap report. Default: Name of the raw data collection in the history" />
                </repeat>
            </when>

                    <param name="name" type="text" label="Name of the group">
                        <validator type="expression" message="A name is required for every group">value.strip()</validator>
                    </param>
                    <repeat name="bam_qc_data" default="1" min="1"
                    title="Data associated with this group">
                        <param name="bam_qc_input" type="data_collection" format="txt" label="Single-sample BAM QC data" help="" collection_type="list" multiple="true" />
                    </repeat>
                </repeat>
            </when>
        </conditional>
    </inputs>