comparison htseq-count.xml @ 5:8a5d43b21c6e

Improved error handling

4:14bec14f4290

    | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}' > $counts 2>$othercounts
    #if $samout_conditional.samout:
        && samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile
    #end if</command>
    <inputs>
        <param format="sam, bam" name="samfile" type="data" label="Aligned SAM File">
            <help>Paired-End data must be sorted by QUERY NAME, use Picard Read Mate Fixer and Query name sort order before using this tool on paired data</help>
        </param>
        <param format="gff" name="gfffile" type="data" label="GFF File"/>
        <param name="mode" type="select" label="Mode">
            <help>Mode to handle reads overlapping more than one feature.</help>
            <option value="union" selected="true">Union</option>

        </param>
        <param name="type" type="text" value="exon" label="Feature type">
            <help>Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon.</help>
        </param>
        <param name="idattr" type="text" value="gene_id" 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 and Ensembl GTF files, is gene_id.</help>
        </param>
        <conditional name="samout_conditional">
            <param name="samout" type="boolean" value="False" truevalue="True" falsevalue="False" label="Additional BAM Output">
                <help>Write out all SAM alignment records into an output BAM file, annotating each line with its assignment to a feature or a special counter (as an optional field with tag ‘XF’).</help>
            </param>

        </data>
    </outputs>

    <stdio>
        <exit_code range="1:" level="fatal" description="Unknown error occurred" />
    </stdio>

    <tests>
        <test>
            <param name="samfile" value="htseq-test.sam" />

5:8a5d43b21c6e

    | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&2"; else print $0}' > $counts 2>$othercounts
    #if $samout_conditional.samout:
        && samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile
    #end if</command>
    <inputs>
        <param format="sam, bam" name="samfile" type="data" label="Aligned SAM/BAM File">
            <help>Paired-End data MUST be sorted by QUERY NAME, use Picard Read Mate Fixer and Query name sort order before using this tool on paired data</help>
        </param>
        <param format="gff" name="gfffile" type="data" label="GFF File"/>
        <param name="mode" type="select" label="Mode">
            <help>Mode to handle reads overlapping more than one feature.</help>
            <option value="union" selected="true">Union</option>

        </param>
        <param name="type" type="text" value="exon" label="Feature type">
            <help>Feature type (3rd column in GFF file) to be used. All features of other types are ignored. The default, suitable for RNA-Seq and Ensembl GTF files, is exon.</help>
        </param>
        <param name="idattr" type="text" value="gene_id" 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. All features of the specified type MUST have a value for this attribute. The default, suitable for RNA-SEq and Ensembl GTF files, is gene_id.</help>
        </param>
        <conditional name="samout_conditional">
            <param name="samout" type="boolean" value="False" truevalue="True" falsevalue="False" label="Additional BAM Output">
                <help>Write out all SAM alignment records into an output BAM file, annotating each line with its assignment to a feature or a special counter (as an optional field with tag ‘XF’).</help>
            </param>

        </data>
    </outputs>

    <stdio>
        <exit_code range="1:" level="fatal" description="Unknown error occurred" />
        <regex match="htseq-count: command not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" />
        <regex match="samtools: command not found" source="stderr" level="fatal" description="The samtools package is not properly installed, contact Galaxy administrators" />
        <regex match="Error: Feature (.+) does not contain a '(.+)' attribute" source="both" level="fatal" description="Error parsing the GFF file, at least one feature of the specified 'Feature type' does not have a value for the specified 'ID Attribute'" />
        <regex match="Error occured in line (\d+) of file" source="stderr" level="fatal" description="Unknown error parsing the GFF file" />
    </stdio>

    <tests>
        <test>
            <param name="samfile" value="htseq-test.sam" />