Mercurial > repos > peterjc > clc_assembly_cell
diff tools/clc_assembly_cell/clc_mapper.xml @ 5:31a9169b6222 draft default tip
"Update all the pico_galaxy tools on main Tool Shed"
| author | peterjc |
|---|---|
| date | Fri, 16 Apr 2021 22:32:53 +0000 |
| parents | 46a667b5e19e |
| children |
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--- a/tools/clc_assembly_cell/clc_mapper.xml Wed Feb 01 07:05:09 2017 -0500 +++ b/tools/clc_assembly_cell/clc_mapper.xml Fri Apr 16 22:32:53 2021 +0000 @@ -1,46 +1,41 @@ -<tool id="clc_mapper" name="CLC Mapper" version="0.0.6"> +<tool id="clc_mapper" name="CLC Mapper" version="0.0.7"> <description>Maps reads giving a SAM/BAM file</description> <requirements> - <requirement type="binary">clc_mapper</requirement> - <requirement type="binary">clc_cas_to_sam</requirement> - <requirement type="binary">samtools</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command>${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command> - <command>echo Mapping reads with clc_mapper... + <version_command> +${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version + </version_command> + <command detect_errors="aggressive"> +echo Mapping reads with clc_mapper... && \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper #for $ref in $references #if str($ref.ref_type)=="circular" --d -z "$ref.ref_file" +-d -z '$ref.ref_file' #else --d "$ref.ref_file" +-d '$ref.ref_file' #end if #end for #for $rg in $read_group ##-------------------------------------- #if str($rg.segments.type) == "paired" --p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2" +-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i '$rg.segments.filename1' '$rg.segments.filename2' #end if ##-------------------------------------- #if str($rg.segments.type) == "interleaved" --p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q "$rg.segments.filename" +-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q '$rg.segments.filename' #end if ##-------------------------------------- #if str($rg.segments.type) == "none" -p no -q #for $f in $rg.segments.filenames -"$f" +'$f' #end for #end if ##-------------------------------------- #end for -o "temp_job.cas" ---cpus \${GALAXY_SLOTS:-4} +--cpus "\${GALAXY_SLOTS:-4}" ## TODO - filtering out the progress lines seems to mess up the multiple commands ## | grep -v "^Progress: " ##=========================================== @@ -48,12 +43,12 @@ ## 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... -&& \${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 +&& \${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" +&& rm 'temp_job.cas' ##=========================================== && echo Sorting BAM file with samtools... && samtools sort "temp_job.bam" "temp_sorted" @@ -147,7 +142,7 @@ <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"/> + <output name="out_bam" 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" /> @@ -160,7 +155,7 @@ <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"/> + <output name="out_bam" file="SRR639755_mito_pairs_vs_NC_010642_clc_u.bam" ftype="bam" lines_diff="4"/> </test> </tests> <help> @@ -190,7 +185,7 @@ <citations> <citation type="bibtex"> @MISC{clcbio, -AUTHOR = {CLC Bio} +AUTHOR = {CLC Bio} title = {{CLC Assembly Cell}}, url = {https://www.qiagenbioinformatics.com/products/clc-assembly-cell/}, year = {2008--2015}