| Previous changeset 4:46a667b5e19e (2017-02-01) |
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Commit message:
"Update all the pico_galaxy tools on main Tool Shed" |
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modified:
tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml tools/clc_assembly_cell/tool_dependencies.xml |
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| diff -r 46a667b5e19e -r 31a9169b6222 tools/clc_assembly_cell/README.rst --- a/tools/clc_assembly_cell/README.rst Wed Feb 01 07:05:09 2017 -0500 +++ b/tools/clc_assembly_cell/README.rst Fri Apr 16 22:32:53 2021 +0000 |
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| @@ -95,6 +95,8 @@ calling ``clc_cas_to_sam`` in the CLC MApper wrapper. v0.0.6 - Update tool XML for optional vs required parameters. - Update URLs in documentation. +v0.0.7 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ====================================================================== @@ -108,17 +110,17 @@ Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ + $ planemo shed_update -t testtoolshed --check_diff tools/clc_assembly_cell/ ... or:: - $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ + $ planemo shed_update -t toolshed --check_diff tools/clc_assembly_cell/ ... To just build and check the tar ball, use:: - $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/clc_assembly_cell/ + $ planemo shed_upload --tar_only tools/clc_assembly_cell/ ... $ tar -tzf shed_upload.tar.gz test-data/NC_010642.fna |
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| diff -r 46a667b5e19e -r 31a9169b6222 tools/clc_assembly_cell/clc_assembler.xml --- a/tools/clc_assembly_cell/clc_assembler.xml Wed Feb 01 07:05:09 2017 -0500 +++ b/tools/clc_assembly_cell/clc_assembler.xml Fri Apr 16 22:32:53 2021 +0000 |
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| @@ -1,15 +1,10 @@ -<tool id="clc_assembler" name="CLC assembler" version="0.0.6"> +<tool id="clc_assembler" name="CLC assembler" version="0.0.7"> <description>Assembles reads giving a FASTA file</description> - <requirements> - <requirement type="binary">clc_assembler</requirement> - </requirements> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command>${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command> - <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler + <version_command> +${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version + </version_command> + <command detect_errors="aggressive"> +\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler #for $rg in $read_group ##-------------------------------------- #if str($rg.segments.type) == "paired" |
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| diff -r 46a667b5e19e -r 31a9169b6222 tools/clc_assembly_cell/clc_mapper.xml --- 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 |
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| @@ -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} |
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| diff -r 46a667b5e19e -r 31a9169b6222 tools/clc_assembly_cell/tool_dependencies.xml --- a/tools/clc_assembly_cell/tool_dependencies.xml Wed Feb 01 07:05:09 2017 -0500 +++ b/tools/clc_assembly_cell/tool_dependencies.xml Fri Apr 16 22:32:53 2021 +0000 |
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| @@ -1,6 +1,6 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="c9bd782f5342"/> </package> -</tool_dependency> +</tool_dependency> \ No newline at end of file |