comparison htseq_count.xml @ 2:db9da9716914 draft

add r-dt

1:cc33706a1d4b

    </requirements>
    <stdio>
        <regex match="XXX" source="stderr" level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command><![CDATA[Rscript '${__tool_directory__}/aurora_htseq_count.R'

			-e $echo
			-o $report
			-d $report.files_path
			-s $sink_message
			-t '${__tool_directory__}'
			
			-f $format
			-r $order
			-S $stranded
			-a $minaqual
			-T $feature_type
			-i $idattr
			-I $additional_attr
			-m $mode]]></command>
    <inputs>
        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
               label="Display analysis code in report?"/>
        <param type="data" name="alignment_file" label="Alignment file (SAM/BAM)" optional="False" format="sam,bam"/>
        <param type="data" name="gff" label="GFF file" optional="False" format="gff, gff3"/>
        <param type="select" name="format" argument="-f" label="Input data format" optional="False" multiple="False">
            <option value="sam" selected="false">SAM</option>
            <option value="bam" selected="false">BAM</option>
        </param>
        <param type="select" name="order" argument="-r" label="Order"
               help="Use this option to indicate how the input data has been sorted. The default is name.&#13;&#10;&#13;&#10;"
               optional="False" multiple="False">
            <option value="name" selected="false">Name</option>
            <option value="pos" selected="false">Position</option>

               help="Feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for RNA-Seq analysis using an Ensembl GTF file: exon)"
               optional="False" value="exon"/>
        <param type="text" name="idattr" argument="-i" label="ID attribute"
               help="GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. The default, suitable for RNA-Seq analysis using an Ensembl GTF file, is gene_id."
               optional="False" value="gene_id"/>
        <param type="text" name="additional_attr" argument="--additional-attr" label="Additional attributes"
               help="Additional feature attributes, which will be printed as an additional column after the primary attribute column but before the counts column(s). The default is none, a suitable value to get gene names using an Ensembl GTF file is gene_name."
               optional="True"/>
        <param type="select" name="mode" argument="-m" label="Mode"
               help="Mode to handle reads overlapping more than one feature. Possible values for &lt;mode&gt; are union, intersection-strict and intersection-nonempty (default: union)"
               optional="False" multiple="False">
            <option value="union" selected="true">Union</option>
            <option value="intersection-strict" selected="false">Intersection (strict)</option>
            <option value="intersection-nonempty" selected="false">Intersection (nonempty)</option>
        </param>
    </inputs>
    <outputs>
        <data name="Aurora htseq" format="html" label="Aurora htseq on ${on_string}" hidden="false"/>
        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
        <data name="count" format="txt" label="Aurora htseq-count on ${on_string}" hidden="false"/>
    </outputs>
    <citations>
        <citation type="bibtex"><![CDATA[

2:db9da9716914

    </requirements>
    <stdio>
        <regex match="XXX" source="stderr" level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command><![CDATA[Rscript '${__tool_directory__}/htseq_count_render.R'

			-e $echo
			-o $report
			-d $report.files_path
			-s $sink_message
			-t '${__tool_directory__}'
			
			-A '$alignment_files'
      -B '$sample_names'
			-G $gff
			-f $format
			-r $order
			-S $stranded
			-a $minaqual
			-T $feature_type
			-i $idattr
			-m $mode
			-c $count]]></command>
    <inputs>
        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
               label="Display analysis code in report?"/>
        <param type="data" name="alignment_files" label="Alignment file (SAM/BAM)" optional="False" format="sam,bam"
               multiple="True"/>
        <param type="text" name="sample_names" label="Sample names"
               help="sample names for each input SAM/BAM file. Use comma to separate multiple names, for example, sample_1, sample_2, sample_3. The number of sample names should be the same as the number of input SAM/BAM files."
               optional="False" size="5x25"/>
        <param type="select" name="format" argument="-f" label="Input data format" optional="False" multiple="False">
            <option value="sam" selected="false">SAM</option>
            <option value="bam" selected="false">BAM</option>
        </param>
        <param type="data" name="gff" label="GFF file" optional="False" format="gff, gff3"/>
        <param type="select" name="order" argument="-r" label="Order"
               help="Use this option to indicate how the input data has been sorted. The default is name.&#13;&#10;&#13;&#10;"
               optional="False" multiple="False">
            <option value="name" selected="false">Name</option>
            <option value="pos" selected="false">Position</option>

               help="Feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for RNA-Seq analysis using an Ensembl GTF file: exon)"
               optional="False" value="exon"/>
        <param type="text" name="idattr" argument="-i" label="ID attribute"
               help="GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. The default, suitable for RNA-Seq analysis using an Ensembl GTF file, is gene_id."
               optional="False" value="gene_id"/>
        <param type="select" name="mode" argument="-m" label="Mode"
               help="Mode to handle reads overlapping more than one feature. Possible values for &lt;mode&gt; are union, intersection-strict and intersection-nonempty (default: union)"
               optional="False" multiple="False">
            <option value="union" selected="true">Union</option>
            <option value="intersection-strict" selected="false">Intersection (strict)</option>
            <option value="intersection-nonempty" selected="false">Intersection (nonempty)</option>
        </param>
    </inputs>
    <outputs>
        <data name="report" format="html" label="Aurora htseq on ${on_string}" hidden="false"/>
        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
        <data name="count" format="txt" label="Aurora htseq-count on ${on_string}" hidden="false"/>
    </outputs>
    <citations>
        <citation type="bibtex"><![CDATA[