Mercurial > repos > peterjc > clc_assembly_cell
changeset 3:9fe1a922353b draft
v0.0.5 option to discard unmapped read; env var bugfix
| author | peterjc |
|---|---|
| date | Wed, 11 May 2016 06:49:58 -0400 |
| parents | 139b6f0a0bb5 |
| children | 46a667b5e19e |
| files | test-data/SRR639755_mito_pairs_vs_NC_010642_clc.bam test-data/SRR639755_mito_pairs_vs_NC_010642_clc_u.bam tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_mapper.xml |
| diffstat | 4 files changed, 25 insertions(+), 3 deletions(-) [+] |
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--- a/tools/clc_assembly_cell/README.rst Tue Sep 01 06:55:13 2015 -0400 +++ b/tools/clc_assembly_cell/README.rst Wed May 11 06:49:58 2016 -0400 @@ -89,6 +89,10 @@ - Added citation tags. - Planemo for Tool Shed upload (``.shed.yml``, internal change only). v0.0.4 - Bug fix for ``<version_command>`` to capture tool version. +v0.0.5 - Support the ``-u`` or ``--discardunmapped`` option to discard + unmapped reads in the CLC Mapper wrapper. + - Bug fix to use the ``$CLC_ASSEMBLY_CELL`` environment variable when + calling ``clc_cas_to_sam`` in the CLC MApper wrapper. ======= ======================================================================
--- a/tools/clc_assembly_cell/clc_mapper.xml Tue Sep 01 06:55:13 2015 -0400 +++ b/tools/clc_assembly_cell/clc_mapper.xml Wed May 11 06:49:58 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="clc_mapper" name="CLC Mapper" version="0.0.4"> +<tool id="clc_mapper" name="CLC Mapper" version="0.0.5"> <description>Maps reads giving a SAM/BAM file</description> <requirements> <requirement type="binary">clc_mapper</requirement> @@ -48,7 +48,11 @@ ## use the offset 33, rather then the CLCbio default of 64 which is only for ## obsolete Illumina FASTQ files. Really need this option per input file... && echo Converting CAS file to BAM with clc_cas_to_sam... -&& /mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/clc_cas_to_sam --cas "temp_job.cas" -o "temp_job.bam" --no-progress --qualityoffset 33 +&& \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_cas_to_sam --cas "temp_job.cas" -o "temp_job.bam" --no-progress --qualityoffset 33 +#if $discard_unmapped: +## -u / --discardunmapped: Discard the unmapped reads +-u +#end if && rm "temp_job.cas" ##=========================================== && echo Sorting BAM file with samtools... @@ -125,7 +129,7 @@ </repeat> <!-- Length fraction (-l), default 0.5 --> <!-- Similarity (-s), default 0.8 --> - <!-- Option for unmapped reads via clc_unmapped_reads ? --> + <param name="discard_unmapped" type="boolean" label="Discard unmappped reads" /> </inputs> <outputs> <data name="out_bam" format="bam" label="CLCbio mapping (BAM)" /> @@ -142,8 +146,22 @@ <param name="read_group_0|segments|max_size" value="1000" /> <param name="read_group_0|segments|dist_mode" value="ss" /> <param name="read_group_0|segments|filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> + <param name="discard_unmapped" value="false" /> <output name="out_fasta" file="SRR639755_mito_pairs_vs_NC_010642_clc.bam" ftype="bam" lines_diff="4"/> </test> + <test> + <param name="ref_file" value="NC_010642.fna" ftype="fasta" /> + <param name="ref_type" value="circular" /> + <param name="read_group_0|segments|type" value="interleaved" /> + <param name="read_group_0|segments|placement" value="fb" /> + <param name="read_group_0|segments|dist_mode" value="ss" /> + <param name="read_group_0|segments|min_size" value="1" /> + <param name="read_group_0|segments|max_size" value="1000" /> + <param name="read_group_0|segments|dist_mode" value="ss" /> + <param name="read_group_0|segments|filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> + <param name="discard_unmapped" value="true" /> + <output name="out_fasta" file="SRR639755_mito_pairs_vs_NC_010642_clc_u.bam" ftype="bam" lines_diff="4"/> + </test> </tests> <help>