comparison multiqc.xml @ 6:01237d721a9f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit d9175b08720c657b7a4521472450dd5ac6fd9361

5:5746cb5cf08d

<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">
    <description>aggregate results from bioinformatics analyses into a single report</description>
    <macros>
        <token name="@WRAPPER_VERSION@">1.2</token>
        <token name="@LN_FILES@">
<![CDATA[
#for $file in $repeat.software_cond.input
    grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
    ln -s '$file' '$software_dir/${file.element_identifier}' &&

        #for $file in $repeat.software_cond.input
            ln -s '${file}' '$software_dir/HiCUP_summary_report_${file.element_identifier}' &&
        #end for
    #elif str($repeat.software_cond.software) == "hisat2"
        #set $pattern = "HISAT2 summary stats:"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "htseq"
        #set $pattern = "__too_low_aQual"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "kallisto"

                    <option value="fastqc">FastQC</option>
                    <option value="featureCounts">featureCounts</option>
                    <option value="flexbar">Flexbar</option>
                    <option value="gatk">GATK (BaseRecalibrator or VariantEval output)</option>
                    <!--<option value="goleft_indexcov">goleft indexcov</option>-->
                    <!--<option value="hicup">HiCUP</option>-->
                    <option value="hisat2">HISAT2</option>
                    <!--<option value="homer">HOMER</option>-->
                    <option value="htseq">HTSeq</option>
                    <!--<option value="jellyfish">Jellyfish</option>-->

                            <option value="base_recalibrator">Base recalibrator file</option>
                        </param>
                        <param name="input" type="data" format="txt" multiple="true" label="GATK output"/>
                    </repeat>
                </when>
                <when value="hisat2">
                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HISAT2" help="It should contain 'HISAT2 summary stats:'"/>
                </when>
                <when value="htseq">
                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HTSeq" help="It should contain '__too_low_aQual'"/>

                    <param name="input" value="hisat2_1.txt,hisat2_2.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="kallisto" />
                    <param name="input" value="kallisto_1.txt,kallisto_2.txt" />
                </conditional>
            </repeat>
            <repeat name="results">

                    <has_text text="bowtie2_se_plot" />
                    <has_text text="hisat2_se_plot" />
                    <has_text text="kallisto_alignment" />
                    <has_text text="star_alignment_plot" />
                    <has_text text="tophat_alignment" />
                </assert_contents>
            </output>
            <output_collection name="stats" type="list">
                <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/>
                <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="0"/>
                <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>
                <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="0"/>
                <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/>
                <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/>
                <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>
            </output_collection>
        </test>

6:01237d721a9f

<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">
    <description>aggregate results from bioinformatics analyses into a single report</description>
    <macros>
        <token name="@WRAPPER_VERSION@">1.3</token>
        <token name="@LN_FILES@">
<![CDATA[
#for $file in $repeat.software_cond.input
    grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
    ln -s '$file' '$software_dir/${file.element_identifier}' &&

        #for $file in $repeat.software_cond.input
            ln -s '${file}' '$software_dir/HiCUP_summary_report_${file.element_identifier}' &&
        #end for
    #elif str($repeat.software_cond.software) == "hisat2"
        #set $pattern = "HISAT2 summary stats:"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "hicexplorer"
        #set $pattern = "Min rest. site distance"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "htseq"
        #set $pattern = "__too_low_aQual"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "kallisto"

                    <option value="fastqc">FastQC</option>
                    <option value="featureCounts">featureCounts</option>
                    <option value="flexbar">Flexbar</option>
                    <option value="gatk">GATK (BaseRecalibrator or VariantEval output)</option>
                    <!--<option value="goleft_indexcov">goleft indexcov</option>-->
                    <option value="hicexplorer">HiCExplorer</option>
                    <!--<option value="hicup">HiCUP</option>-->
                    <option value="hisat2">HISAT2</option>
                    <!--<option value="homer">HOMER</option>-->
                    <option value="htseq">HTSeq</option>
                    <!--<option value="jellyfish">Jellyfish</option>-->

                            <option value="base_recalibrator">Base recalibrator file</option>
                        </param>
                        <param name="input" type="data" format="txt" multiple="true" label="GATK output"/>
                    </repeat>
                </when>
                <when value="hicexplorer">
                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HiCExplorer" help="It should contain 'Min rest. site distance'"/>
                </when>
                <when value="hisat2">
                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HISAT2" help="It should contain 'HISAT2 summary stats:'"/>
                </when>
                <when value="htseq">
                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HTSeq" help="It should contain '__too_low_aQual'"/>

                    <param name="input" value="hisat2_1.txt,hisat2_2.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="hicexplorer" />
                    <param name="input" value="hicexplorer1.log,hicexplorer2.log" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="kallisto" />
                    <param name="input" value="kallisto_1.txt,kallisto_2.txt" />
                </conditional>
            </repeat>
            <repeat name="results">

                    <has_text text="bowtie2_se_plot" />
                    <has_text text="hisat2_se_plot" />
                    <has_text text="kallisto_alignment" />
                    <has_text text="star_alignment_plot" />
                    <has_text text="tophat_alignment" />
                    <has_text text="hicexplorer" />
                    
                </assert_contents>
            </output>
            <output_collection name="stats" type="list">
                <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/>
                <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="0"/>
                <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>
                <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="0"/>
                <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> -->
                <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/>
                <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/>
                <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>
            </output_collection>
        </test>