| Previous changeset 5:8a5d43b21c6e (2012-09-20) Next changeset 7:55bd18f8429c (2012-09-21) |
|
Commit message:
Fix issue with workflows (type->featuretype) and general error check |
|
modified:
htseq-count.xml |
| b |
| diff -r 8a5d43b21c6e -r 2861eb44fbbf htseq-count.xml --- a/htseq-count.xml Thu Sep 20 12:41:53 2012 -0400 +++ b/htseq-count.xml Fri Sep 21 17:40:40 2012 -0400 |
| b |
| @@ -25,7 +25,7 @@ --mode=$mode --stranded=$stranded --minaqual=$minaqual - --type=$type + --type=$featuretype --idattr=$idattr #if $samout_conditional.samout: --samout=$__new_file_path__/${samoutfile.id}_tmp @@ -42,7 +42,7 @@ #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> + <help>Paired-End data MUST be sorted by QUERY NAME, use "NGS: Picard - Paired Read Mate Fixer" to sort by QUERY NAME and output to SAM (not BAM) 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"> @@ -60,7 +60,7 @@ <param name="minaqual" type="integer" value="0" label="Minimum alignment quality"> <help>Skip all reads with alignment quality lower than the given minimum value</help> </param> - <param name="type" type="text" value="exon" label="Feature type"> + <param name="featuretype" 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"> @@ -106,6 +106,7 @@ <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" /> + <regex match="Error" source="stderr" level="fatal" description="Unknown error occured" /> </stdio> <tests> |