Mercurial > repos > vimalkumarvelayudhan > riboplot
diff ribocount.xml @ 4:1901dcdc12ff
Move galaxy xml wrappers to top level
author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
---|---|
date | Wed, 12 Aug 2015 09:44:36 +0100 |
parents | galaxy/ribocount.xml@8e1efafa6277 |
children | 844eb8c36f32 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribocount.xml Wed Aug 12 09:44:36 2015 +0100 @@ -0,0 +1,30 @@ +<tool id="ribocount" name="ribocount" version="0.1.0"> + <description>Get read counts for all transcripts in an alignment (BAM) + </description> + <requirements> + <requirement type="package" version="0.8.3">pysam</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <command interpreter="python">riboplot/ribocount.py + --ribo_file "${ribo_file}" + --transcriptome_fasta "${transcriptome_fasta}" + --read_length "${read_length}" + --read_offset "${read_offset}" + --html_file "${html_file}" + --output_path "${html_file.files_path}" + ## --debug + </command> + <inputs> + <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> + <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> + <param name="read_length" type="integer" label="Read length to consider" value="28"/> + <param name="read_offset" type="integer" label="Offset" value="0"/> + </inputs> + <outputs> + <data format="html" name="html_file" label="ribocount (HTML report)"/> + </outputs> + <help> + </help> +</tool>