Mercurial > repos > peterjc > seq_filter_by_mapping
changeset 13:37de286fc844 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping commit 9ba9eed9534b49378a4f5c53650f30810d3dcd9c-dirty
author | peterjc |
---|---|
date | Wed, 17 May 2017 14:03:07 -0400 |
parents | fb21ab9bdb98 |
children | 1ccb3fea40ba |
files | tools/seq_filter_by_mapping/seq_filter_by_mapping.xml |
diffstat | 1 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml Wed May 17 12:42:03 2017 -0400 +++ b/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml Wed May 17 14:03:07 2017 -0400 @@ -21,7 +21,7 @@ </command> <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." /> - <param name="mapping_file" type="data" format="sam,bam" multiple="true" label="SAM/BAM mapping of those sequences" help="SAM or BAM format." /> + <param name="mapping_file" type="data" format="sam,bam" multiple="true" label="SAM/BAM mapping of those sequences" help="SAM or BAM format." /> <conditional name="output_choice_cond"> <param name="output_choice" type="select" label="Output mapped reads, unmapped reads, or both?"> <option value="both">Both mapped and unmapped reads, as two files</option> @@ -33,12 +33,12 @@ <when value="pos" /> <when value="neg" /> </conditional> - <param name="pair_mode" type="select" label="Paired read treatment"> + <param name="pair_mode" type="select" label="Paired read treatment"> <option value="lax" selected="true">Treat as a pair, allow either read to be mapped</option> - <option value="strict">Treat as a pair, require both reads to be mapped</option> - <!-- The following would actually be more work as have to store qname/1 and qname/2 separately for filter... + <option value="strict">Treat as a pair, require both reads to be mapped</option> + <!-- The following would actually be more work as have to store qname/1 and qname/2 separately for filter... <option value="solo">Treat independently (will split partners when only one maps)</option> - --> + --> </param> </inputs> <outputs> @@ -50,14 +50,14 @@ </data> </outputs> <tests> - <test> + <test> <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" /> <param name="pair_mode" value="lax" /> <param name="output_choice" value="pos" /> <output name="output_pos" file="SRR639755_sample_lax.fastq" ftype="fastqsanger" /> </test> - <test> + <test> <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" /> <param name="pair_mode" value="strict" />